@@ -1,7 +1,7 @@

 Package: lineagespot

 Title: Detection of SARS-CoV-2 lineages in wastewater samples using 

     next-generation sequencing

-Version: 0.99.3

+Version: 0.99.4

 Authors@R: c(

     person(given = "Nikolaos",

             family = "Pechlivanis",

@@ -37,9 +37,11 @@ Encoding: UTF-8

 LazyData: false

 Roxygen: list(markdown = TRUE)

 RoxygenNote: 7.1.2

-biocViews: VariantDetection, VariantAnnotation

+biocViews: VariantDetection, VariantAnnotation, Sequencing

 Imports:

     VariantAnnotation,

+    MatrixGenerics,

+    SummarizedExperiment,

     data.table,

     stringr,

     httr

@@ -7,6 +7,10 @@ export(merge_vcf)

 export(uniq_variants)

 import(data.table)

 import(stringr)

+importFrom(MatrixGenerics,rowRanges)

+importFrom(SummarizedExperiment,assays)

+importFrom(VariantAnnotation,fixed)

+importFrom(VariantAnnotation,info)

 importFrom(VariantAnnotation,readVcf)

 importFrom(httr,GET)

 importFrom(httr,content)

@@ -41,12 +41,14 @@ get_lineage_report <- function(lineages, base.url = "https://api.outbreak.info/g

             strain$`amino acid` = str_split(strain$mutation, "\\:",

                                             simplify = TRUE)[,2]

+            

+            who = which(strain$type != "deletion")

-            strain[which(strain$type != "deletion"), ]$`amino acid` = str_to_upper(strain[which(strain$type != "deletion"), ]$`amino acid`)

+            strain[who, ]$`amino acid` = str_to_upper(strain[who,]$`amino acid`)

             strain$barcode = paste0(strain$gene, ":", strain$`amino acid`)

-            strain[which(strain$type != "deletion"), ]$type = "snp"

+            strain[who, ]$type = "snp"

             out[[l]] = strain

@@ -29,11 +29,13 @@

 #'

 #' @param AF_threshold

 #' A parameter indicating the AF threshold for identifying variants per sample

-#'

-#' @importFrom httr GET content

+#' 

 #' @import data.table

 #' @import stringr

-#' @importFrom VariantAnnotation readVcf

+#' @importFrom httr GET content

+#' @importFrom VariantAnnotation readVcf info fixed 

+#' @importFrom SummarizedExperiment assays

+#' @importFrom MatrixGenerics rowRanges

 #'

 #' @return

 #' A list of three elements;

@@ -70,13 +70,13 @@ lineagespot_hits <- function(vcf_table = NULL,

     aa_variants = str_split(vcf_table$AA_alt, "[0-9]|_")

     codon_num = str_split(vcf_table$AA_alt, "[A-Z]|[a-z]|\\_|\\*|\\?")

-    aa_variants = base::lapply(aa_variants, function(x) {

+    aa_variants = lapply(aa_variants, function(x) {

         return( x[x != ""] )

     })

-    codon_num = base::lapply(codon_num, function(x) {

+    codon_num = lapply(codon_num, function(x) {

         return( x[x != ""] )

@@ -88,11 +88,11 @@ lineagespot_hits <- function(vcf_table = NULL,

     aa_split_list = lapply(seq_len(nrow(vcf_table)), function(i) {

         out = data.table(ref_aa = NA,

-        alt_aa = NA,

-        info = NA,

-        codon_num = NA,

-        codon_start = NA,

-        codon_end = NA)

+                         alt_aa = NA,

+                         info = NA,

+                         codon_num = NA,

+                         codon_start = NA,

+                         codon_end = NA)

         if(length(aa_variants[[i]]) == 2) {

@@ -177,7 +177,7 @@ lineagespot_hits <- function(vcf_table = NULL,

         aa_variants = str_split(ref$`amino acid`, "[0-9]|_|\\/")

         codon_num = str_split(ref$`amino acid`, "[A-Z]|[a-z]|\\_|\\*|\\?|\\/")

-        aa_variants = base::lapply(aa_variants, function(x) {

+        aa_variants = lapply(aa_variants, function(x) {

         x = x[x != ""]

@@ -187,7 +187,7 @@ lineagespot_hits <- function(vcf_table = NULL,

         })

-        codon_num = base::lapply(codon_num, function(x) {

+        codon_num = lapply(codon_num, function(x) {

             return( as.numeric(x[x != ""]) )

@@ -141,9 +141,9 @@ vcf_to_table <- function(x) {

     # vcfR::extract_gt_tidy(x, verbose = FALSE),

     # vcfR::extract_info_tidy(x))

-    out = cbind(as.data.frame(x@rowRanges),

-                as.data.frame(x@fixed),

-                as.data.frame(x@info))

+    out = cbind(as.data.frame(rowRanges(x)),

+                as.data.frame(fixed(x)),

+                as.data.frame(info(x)))

     out$ALT = unlist(lapply(out$ALT, function(x){ return(paste(as.character(x), collapse = ",")) }))

@@ -151,7 +151,7 @@ vcf_to_table <- function(x) {

     out$ID = row.names(out)

-    out$AD = unlist(lapply(x@assays@data$AD, function(x) {return(paste(x, collapse = ","))}))

+    out$AD = unlist(lapply(assays(x)[["AD"]], function(x) {return(paste(x, collapse = ","))}))

     out = setDT(out)

@@ -209,16 +209,16 @@ break_multiple_variants <- function(x) {

         out[[i]] = data.table(CHROM = x[who, ]$CHROM,

-        POS = x[who, ]$POS,

-        ID = x[who, ]$ID,

-        REF = x[who, ]$REF,

-        ALT = ALT_matrix[who, i],

-        DP = x[who, ]$DP,

-        AD_ref = AD_matrix[who, 1],

-        AD_alt = AD_matrix[who, i+1],

-        Gene_Name = x[who, ]$Gene_Name,

-        Nt_alt = x[who, ]$Nt_alt,

-        AA_alt = x[who, ]$AA_alt)

+                              POS = x[who, ]$POS,

+                              ID = x[who, ]$ID,

+                              REF = x[who, ]$REF,

+                              ALT = ALT_matrix[who, i],

+                              DP = x[who, ]$DP,

+                              AD_ref = AD_matrix[who, 1],

+                              AD_alt = AD_matrix[who, i+1],

+                              Gene_Name = x[who, ]$Gene_Name,

+                              Nt_alt = x[who, ]$Nt_alt,

+                              AA_alt = x[who, ]$AA_alt)

     }

@@ -1,10 +1,10 @@

 ##fileformat=VCFv4.2

-##fileDate=20210323

-##source=freeBayes v1.2.0-dirty

+##fileDate=20210401

+##source=freeBayes v1.3.2-dirty

 ##reference=/work/nikospech/SARS-CoV-2/ref/NC_045512.fasta

 ##contig=<ID=NC_045512.2,length=29903>

 ##phasing=none

-##commandline="freebayes -f /work/nikospech/SARS-CoV-2/ref/NC_045512.fasta -F 0.01 -C 1 --pooled-continuous CoV19_L1_S1_sorted_uniq.bam"

+##commandline="freebayes -f /work/nikospech/SARS-CoV-2/ref/NC_045512.fasta -F 0.01 -C 1 --pooled-continuous L4_S1_L001_sorted_uniq.bam"

 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">

 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">

 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">

@@ -59,400 +59,589 @@

 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">

 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">

 ##SnpEffVersion="5.0 (build 2020-08-09 21:23), by Pablo Cingolani"

-##SnpEffCmd="SnpEff  NC_045512.2 CoV19_L1_S1_freebayes.vcf "

+##SnpEffCmd="SnpEff  NC_045512.2 L4_S1_L001_freebayes.vcf "

 ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">

 ##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">

 ##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">

 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown

-NC_045512.2	326	.	T	A	1.46332E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.2982;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=210;RO=6;RPL=0;RPP=5.18177;RPPR=16.0391;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=16.0391;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.61T>A|p.Leu21Ile|61/21291|61/21291|21/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.61T>A|p.Leu21Ile|61/540|61/540|21/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.61T>A|p.Leu21Ile|61/540|61/540|21/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.61T>A|p.Leu21Ile|61/13218|61/13218|21/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-480T>A|||||480|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-480T>A|||||480|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2394T>A|||||2394|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2394T>A|||||2394|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:7:6,1:6:210:1:18:0,-0.307237,-17.4415

-NC_045512.2	378	.	T	C	1.30042E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.0214;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=336;RO=9;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.113T>C|p.Val38Ala|113/21291|113/21291|38/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.113T>C|p.Val38Ala|113/540|113/540|38/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.113T>C|p.Val38Ala|113/540|113/540|38/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.113T>C|p.Val38Ala|113/13218|113/13218|38/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-428T>C|||||428|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-428T>C|||||428|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2342T>C|||||2342|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2342T>C|||||2342|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:336:1:14:0,-1.61031,-29.1938

-NC_045512.2	408	.	A	T	2.59462E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.3306;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=349;RO=9;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.143A>T|p.Asp48Val|143/21291|143/21291|48/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.143A>T|p.Asp48Val|143/540|143/540|48/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.143A>T|p.Asp48Val|143/540|143/540|48/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.143A>T|p.Asp48Val|143/13218|143/13218|48/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-398A>T|||||398|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-398A>T|||||398|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2312A>T|||||2312|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2312A>T|||||2312|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:349:1:17:0,-1.31032,-30.0709

-NC_045512.2	433	.	T	C	0.00484947	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.79688;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=306;RO=8;RPL=0;RPP=7.35324;RPPR=20.3821;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=20.3821;SRR=0;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.168T>C|p.Val56Val|168/21291|168/21291|56/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.168T>C|p.Val56Val|168/540|168/540|56/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.168T>C|p.Val56Val|168/540|168/540|56/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.168T>C|p.Val56Val|168/13218|168/13218|56/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-373T>C|||||373|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-373T>C|||||373|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2287T>C|||||2287|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2287T>C|||||2287|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:306:2:55:-2.21142,0,-24.8895

-NC_045512.2	442	.	C	T	2.061E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5609;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=349;RO=9;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.177C>T|p.Gly59Gly|177/21291|177/21291|59/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.177C>T|p.Gly59Gly|177/540|177/540|59/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.177C>T|p.Gly59Gly|177/540|177/540|59/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.177C>T|p.Gly59Gly|177/13218|177/13218|59/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-364C>T|||||364|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-364C>T|||||364|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2278C>T|||||2278|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2278C>T|||||2278|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:349:1:16:0,-1.41032,-30.1708

-NC_045512.2	445	.	T	C	241.632	.	AB=0.9;ABP=16.9077;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.95964;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=36;RO=1;RPL=3;RPP=5.18177;RPPR=5.18177;RPR=6;RUN=1;SAF=9;SAP=22.5536;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.180T>C|p.Val60Val|180/21291|180/21291|60/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.180T>C|p.Val60Val|180/540|180/540|60/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.180T>C|p.Val60Val|180/540|180/540|60/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.180T>C|p.Val60Val|180/13218|180/13218|60/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-361T>C|||||361|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-361T>C|||||361|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2275T>C|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2275T>C|||||2275|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:1,9:1:36:9:342:-28.1273,0,-0.587975

-NC_045512.2	476	.	A	G	3.43906E-7	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=7.35324;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.3515;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=718;RO=19;RPL=0;RPP=7.35324;RPPR=3.12459;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.211A>G|p.Ile71Val|211/21291|211/21291|71/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.211A>G|p.Ile71Val|211/540|211/540|71/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.211A>G|p.Ile71Val|211/540|211/540|71/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.211A>G|p.Ile71Val|211/13218|211/13218|71/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-330A>G|||||330|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-330A>G|||||330|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2244A>G|||||2244|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2244A>G|||||2244|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:718:2:74:-0.704246,0,-58.63

-NC_045512.2	529	.	G	T	2.12537E-6	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=7.35324;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=721;RO=19;RPL=1;RPP=3.0103;RPPR=3.12459;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=9;SRP=3.12459;SRR=10;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.264G>T|p.Leu88Leu|264/21291|264/21291|88/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.264G>T|p.Leu88Leu|264/540|264/540|88/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.264G>T|p.Leu88Leu|264/540|264/540|88/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.264G>T|p.Leu88Leu|264/13218|264/13218|88/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-277G>T|||||277|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-277G>T|||||277|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2191G>T|||||2191|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2191G>T|||||2191|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:721:2:76:-0.893181,0,-58.9014

-NC_045512.2	548	.	A	G	2.04288E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.7801;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=754;RO=20;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.283A>G|p.Ile95Val|283/21291|283/21291|95/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.283A>G|p.Ile95Val|283/540|283/540|95/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.283A>G|p.Ile95Val|283/540|283/540|95/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.283A>G|p.Ile95Val|283/13218|283/13218|95/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-258A>G|||||258|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-258A>G|||||258|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2172A>G|||||2172|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2172A>G|||||2172|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:754:1:39:0,-2.42507,-64.2908

-NC_045512.2	649	.	TAAAGGAGC	TAAGGAGC,CAAAGGAGC	9.97311E-13	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D7M,1X8M;DP=25;DPB=24.8889;DPRA=0,0;EPP=5.18177,5.18177;EPPR=52.9542;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=29.7225;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=34,33;QR=861;RO=23;RPL=0,0;RPP=5.18177,5.18177;RPPR=3.10471;RPR=1,1;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=12;SRP=3.10471;SRR=11;TYPE=del,snp;ANN=TAAGGAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.387delA|p.Gly130fs|387/21291|387/21291|129/7096||,TAAGGAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.387delA|p.Gly130fs|387/540|387/540|129/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TAAGGAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.387delA|p.Gly130fs|387/540|387/540|129/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TAAGGAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.387delA|p.Gly130fs|387/13218|387/13218|129/4405||,CAAAGGAGC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.384T>C|p.Asn128Asn|384/21291|384/21291|128/7096||,CAAAGGAGC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.384T>C|p.Asn128Asn|384/540|384/540|128/179||WARNING_TRANSCRIPT_NO_STOP_CODON,CAAAGGAGC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.384T>C|p.Asn128Asn|384/540|384/540|128/179||WARNING_TRANSCRIPT_NO_STOP_CODON,CAAAGGAGC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.384T>C|p.Asn128Asn|384/13218|384/13218|128/4405||,CAAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-157T>C|||||157|WARNING_TRANSCRIPT_NO_START_CODON,TAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-154delA|||||154|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-157T>C|||||157|WARNING_TRANSCRIPT_NO_START_CODON,TAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-154delA|||||154|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2071T>C|||||2071|WARNING_TRANSCRIPT_NO_START_CODON,TAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2068delA|||||2068|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2071T>C|||||2071|WARNING_TRANSCRIPT_NO_START_CODON,TAAGGAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2068delA|||||2068|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:23,1,1:23:861:1,1:34,33:0,-4.16071,-74.4153,-4.26049,-72.05,-74.5055

-NC_045512.2	706	.	C	A	3.73074E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.7763;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1055;RO=28;RPL=0;RPP=5.18177;RPPR=5.80219;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=5.80219;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.441C>A|p.Asp147Glu|441/21291|441/21291|147/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.441C>A|p.Asp147Glu|441/540|441/540|147/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.441C>A|p.Asp147Glu|441/540|441/540|147/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.441C>A|p.Asp147Glu|441/13218|441/13218|147/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-100C>A|||||100|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-100C>A|||||100|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2014C>A|||||2014|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2014C>A|||||2014|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:29:28,1:28:1055:1:38:0,-4.9326,-91.4639

-NC_045512.2	712	.	T	A	4.4525E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=7.35324;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2106;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=1040;RO=27;RPL=2;RPP=7.35324;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=18;SRP=9.52472;SRR=9;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.447T>A|p.Leu149Leu|447/21291|447/21291|149/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.447T>A|p.Leu149Leu|447/540|447/540|149/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.447T>A|p.Leu149Leu|447/540|447/540|149/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.447T>A|p.Leu149Leu|447/13218|447/13218|149/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-94T>A|||||94|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-94T>A|||||94|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2008T>A|||||2008|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2008T>A|||||2008|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:29:27,2:27:1040:2:40:0,-4.92995,-90.1093

-NC_045512.2	716	.	A	G	3.73074E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.7763;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1061;RO=28;RPL=0;RPP=5.18177;RPPR=5.80219;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=5.80219;SRR=11;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.451A>G|p.Thr151Ala|451/21291|451/21291|151/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.451A>G|p.Thr151Ala|451/540|451/540|151/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.451A>G|p.Thr151Ala|451/540|451/540|151/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.451A>G|p.Thr151Ala|451/13218|451/13218|151/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-90A>G|||||90|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-90A>G|||||90|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2004A>G|||||2004|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2004A>G|||||2004|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:29:28,1:28:1061:1:38:0,-4.9326,-92.001

-NC_045512.2	792	.	A	G	3.26967E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2259;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1264;RO=34;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.527A>G|p.Glu176Gly|527/21291|527/21291|176/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.527A>G|p.Glu176Gly|527/540|527/540|176/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.527A>G|p.Glu176Gly|527/540|527/540|176/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.527A>G|p.Glu176Gly|527/13218|527/13218|176/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-14A>G|||||14|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-14A>G|||||14|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1928A>G|||||1928|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1928A>G|||||1928|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,2:34:1264:2:76:0,-3.62227,-106.838

-NC_045512.2	852	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.7841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1288;RO=35;RPL=0;RPP=5.18177;RPPR=3.07234;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.587A>C|p.Tyr196Ser|587/21291|587/21291|196/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.587A>C|p.Tyr196Ser|587/13218|587/13218|196/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.47A>C|p.Tyr16Ser|47/1914|47/1914|16/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.47A>C|p.Tyr16Ser|47/1914|47/1914|16/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1868A>C|||||1868|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1868A>C|||||1868|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*47A>C|||||47|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*47A>C|||||47|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1288:1:14:0,-9.43709,-114.813

-NC_045512.2	949	.	ATA	AA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=34;DPB=33.6667;DPRA=0;EPP=5.18177;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.7777;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1225;RO=33;RPL=0;RPP=5.18177;RPPR=3.60252;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.60252;SRR=18;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.685delT|p.Tyr229fs|685/21291|685/21291|229/7096||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.685delT|p.Tyr229fs|685/13218|685/13218|229/4405||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.145delT|p.Tyr49fs|145/1914|145/1914|49/637||WARNING_TRANSCRIPT_NO_START_CODON,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.145delT|p.Tyr49fs|145/1914|145/1914|49/637||WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1770delT|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1770delT|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*145delT|||||145|WARNING_TRANSCRIPT_NO_STOP_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*145delT|||||145|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:33,1:33:1225:1:37:0,-6.53719,-106.849

-NC_045512.2	959	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.1297;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1411;RO=37;RPL=0;RPP=5.18177;RPPR=3.06899;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.694C>T|p.Arg232Cys|694/21291|694/21291|232/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.694C>T|p.Arg232Cys|694/13218|694/13218|232/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.154C>T|p.Arg52Cys|154/1914|154/1914|52/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.154C>T|p.Arg52Cys|154/1914|154/1914|52/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1761C>T|||||1761|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1761C>T|||||1761|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*154C>T|||||154|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*154C>T|||||154|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1411:1:33:0,-8.14,-123.976

-NC_045512.2	969	.	A	G	4.94241E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.1144;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1472;RO=38;RPL=1;RPP=5.18177;RPPR=3.9246;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.9246;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.704A>G|p.Glu235Gly|704/21291|704/21291|235/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.704A>G|p.Glu235Gly|704/13218|704/13218|235/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.164A>G|p.Glu55Gly|164/1914|164/1914|55/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.164A>G|p.Glu55Gly|164/1914|164/1914|55/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1751A>G|||||1751|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1751A>G|||||1751|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*164A>G|||||164|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*164A>G|||||164|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1472:1:39:0,-7.84361,-128.858

-NC_045512.2	991	.	G	T	9.73415E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.343;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1460;RO=38;RPL=0;RPP=5.18177;RPPR=3.23888;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.23888;SRR=18;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.726G>T|p.Thr242Thr|726/21291|726/21291|242/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.726G>T|p.Thr242Thr|726/13218|726/13218|242/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.186G>T|p.Thr62Thr|186/1914|186/1914|62/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.186G>T|p.Thr62Thr|186/1914|186/1914|62/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1729G>T|||||1729|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1729G>T|||||1729|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*186G>T|||||186|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*186G>T|||||186|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1460:1:38:0,-7.9429,-127.883

-NC_045512.2	1044	.	C	A	6.0404E-4	.	AB=0.136364;ABP=28.2783;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=9.52472;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.88035;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=117;QR=740;RO=19;RPL=0;RPP=9.52472;RPPR=44.2683;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=19;SRP=44.2683;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.779C>A|p.Ala260Glu|779/21291|779/21291|260/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.779C>A|p.Ala260Glu|779/13218|779/13218|260/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.239C>A|p.Ala80Glu|239/1914|239/1914|80/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.239C>A|p.Ala80Glu|239/1914|239/1914|80/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1676C>A|||||1676|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1676C>A|||||1676|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*239C>A|||||239|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*239C>A|||||239|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:22:19,3:19:740:3:117:-4.28772,0,-60.3084

-NC_045512.2	1055	.	G	A	3.38927E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.5775;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=814;RO=21;RPL=0;RPP=5.18177;RPPR=48.6112;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=48.6112;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.790G>A|p.Asp264Asn|790/21291|790/21291|264/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.790G>A|p.Asp264Asn|790/13218|790/13218|264/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.250G>A|p.Asp84Asn|250/1914|250/1914|84/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.250G>A|p.Asp84Asn|250/1914|250/1914|84/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1665G>A|||||1665|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1665G>A|||||1665|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*250G>A|||||250|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*250G>A|||||250|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:814:1:37:0,-2.92483,-69.8873

-NC_045512.2	1069	.	G	A	5.35018E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.1199;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=809;RO=21;RPL=0;RPP=5.18177;RPPR=5.59539;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=48.6112;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.804G>A|p.Gly268Gly|804/21291|804/21291|268/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.804G>A|p.Gly268Gly|804/13218|804/13218|268/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.264G>A|p.Gly88Gly|264/1914|264/1914|88/637||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.264G>A|p.Gly88Gly|264/1914|264/1914|88/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1651G>A|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1651G>A|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*264G>A|||||264|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*264G>A|||||264|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:809:1:39:0,-2.7261,-69.2377

-NC_045512.2	1112	.	A	G	6.14782E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=87.8997;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.4435;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1652;RO=43;RPL=0;RPP=5.18177;RPPR=3.0608;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0608;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.847A>G|p.Thr283Ala|847/21291|847/21291|283/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.847A>G|p.Thr283Ala|847/13218|847/13218|283/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.307A>G|p.Thr103Ala|307/1914|307/1914|103/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.307A>G|p.Thr103Ala|307/1914|307/1914|103/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1608A>G|||||1608|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1608A>G|||||1608|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*307A>G|||||307|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*307A>G|||||307|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1652:1:15:0,-11.7453,-147.44

-NC_045512.2	1185	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=7.35324;EPPR=94.2121;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.6925;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1561;RO=42;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.920C>T|p.Ala307Val|920/21291|920/21291|307/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.920C>T|p.Ala307Val|920/13218|920/13218|307/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.380C>T|p.Ala127Val|380/1914|380/1914|127/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.380C>T|p.Ala127Val|380/1914|380/1914|127/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1535C>T|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1535C>T|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*380C>T|||||380|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*380C>T|||||380|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:42,2:42:1561:2:77:0,-5.93618,-133.453

-NC_045512.2	1323	.	G	A	3.73981E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.3577;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1104;RO=29;RPL=1;RPP=5.18177;RPPR=15.6647;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=15.6647;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1058G>A|p.Gly353Asp|1058/21291|1058/21291|353/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1058G>A|p.Gly353Asp|1058/13218|1058/13218|353/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.518G>A|p.Gly173Asp|518/1914|518/1914|173/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.518G>A|p.Gly173Asp|518/1914|518/1914|173/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1397G>A|||||1397|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1397G>A|||||1397|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*518G>A|||||518|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*518G>A|||||518|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1104:1:37:0,-5.33307,-95.9692

-NC_045512.2	1336	.	T	G	2.14139E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.0362;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=743;RO=21;RPL=1;RPP=5.18177;RPPR=5.59539;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=5.59539;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1071T>G|p.Cys357Trp|1071/21291|1071/21291|357/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1071T>G|p.Cys357Trp|1071/13218|1071/13218|357/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.531T>G|p.Cys177Trp|531/1914|531/1914|177/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.531T>G|p.Cys177Trp|531/1914|531/1914|177/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1384T>G|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1384T>G|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*531T>G|||||531|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*531T>G|||||531|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:743:1:35:0,-3.12403,-63.6907

-NC_045512.2	1430	.	A	T	1.69883E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.9646;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=611;RO=16;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=3.0103;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1165A>T|p.Asn389Tyr|1165/21291|1165/21291|389/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1165A>T|p.Asn389Tyr|1165/13218|1165/13218|389/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.625A>T|p.Asn209Tyr|625/1914|625/1914|209/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.625A>T|p.Asn209Tyr|625/1914|625/1914|209/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1290A>T|||||1290|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1290A>T|||||1290|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*625A>T|||||625|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*625A>T|||||625|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:611:1:15:0,-3.61752,-53.8289

-NC_045512.2	1513	.	C	T	9.34061E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.0497;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=306;RO=8;RPL=0;RPP=5.18177;RPPR=20.3821;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=20.3821;SRR=8;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1248C>T|p.Cys416Cys|1248/21291|1248/21291|416/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1248C>T|p.Cys416Cys|1248/13218|1248/13218|416/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.708C>T|p.Cys236Cys|708/1914|708/1914|236/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.708C>T|p.Cys236Cys|708/1914|708/1914|236/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1207C>T|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1207C>T|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*708C>T|||||708|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*708C>T|||||708|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:9:8,1:8:306:1:17:0,-1.00929,-26.2008

-NC_045512.2	1618	.	T	C	1.26801E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.3492;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=584;RO=15;RPL=1;RPP=5.18177;RPPR=3.15506;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.15506;SRR=8;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1353T>C|p.Leu451Leu|1353/21291|1353/21291|451/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1353T>C|p.Leu451Leu|1353/13218|1353/13218|451/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.813T>C|p.Leu271Leu|813/1914|813/1914|271/637||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.813T>C|p.Leu271Leu|813/1914|813/1914|271/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1102T>C|||||1102|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1102T>C|||||1102|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*813T>C|||||813|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*813T>C|||||813|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:584:1:38:0,-1.01921,-49.106

-NC_045512.2	1634	.	GAG	GG	1.26801E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=16;DPB=15.6667;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.3492;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=570;RO=15;RPL=1;RPP=5.18177;RPPR=3.15506;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.15506;SRR=8;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1370delA|p.Glu457fs|1370/21291|1370/21291|457/7096||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1370delA|p.Glu457fs|1370/13218|1370/13218|457/4405||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.830delA|p.Glu277fs|830/1914|830/1914|277/637||WARNING_TRANSCRIPT_NO_START_CODON,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.830delA|p.Glu277fs|830/1914|830/1914|277/637||WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1085delA|||||1085|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1085delA|||||1085|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*830delA|||||830|WARNING_TRANSCRIPT_NO_STOP_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*830delA|||||830|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:570:1:38:0,-1.01921,-47.8456

-NC_045512.2	1706	.	T	A	1.84217E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.0679;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=234;RO=6;RPL=1;RPP=5.18177;RPPR=16.0391;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=16.0391;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1441T>A|p.Ser481Thr|1441/21291|1441/21291|481/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1441T>A|p.Ser481Thr|1441/13218|1441/13218|481/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.901T>A|p.Ser301Thr|901/1914|901/1914|301/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.901T>A|p.Ser301Thr|901/1914|901/1914|301/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1014T>A|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1014T>A|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*901T>A|||||901|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*901T>A|||||901|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:7:6,1:6:234:1:19:0,-0.207244,-19.5311

-NC_045512.2	1725	.	T	C	5.64903E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.4603;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=501;RO=13;RPL=0;RPP=5.18177;RPPR=3.17734;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1460T>C|p.Phe487Ser|1460/21291|1460/21291|487/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1460T>C|p.Phe487Ser|1460/13218|1460/13218|487/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.920T>C|p.Phe307Ser|920/1914|920/1914|307/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.920T>C|p.Phe307Ser|920/1914|920/1914|307/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-995T>C|||||995|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-995T>C|||||995|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*920T>C|||||920|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*920T>C|||||920|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:501:1:13:0,-2.91443,-44.1387

-NC_045512.2	2048	.	C	T	112.072	.	AB=0.428571;ABP=3.63072;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=16.0391;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.8054;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=229;QR=310;RO=8;RPL=3;RPP=3.0103;RPPR=3.0103;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1783C>T|p.Leu595Leu|1783/21291|1783/21291|595/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1783C>T|p.Leu595Leu|1783/13218|1783/13218|595/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1243C>T|p.Leu415Leu|1243/1914|1243/1914|415/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1243C>T|p.Leu415Leu|1243/1914|1243/1914|415/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-672C>T|||||672|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-672C>T|||||672|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1243C>T|||||1243|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1243C>T|||||1243|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:14:8,6:8:310:6:229:-16.7605,0,-24.0493

-NC_045512.2	2514	.	A	T	2.061E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5609;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=343;RO=9;RPL=0;RPP=5.18177;RPPR=3.25157;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2249A>T|p.Glu750Val|2249/21291|2249/21291|750/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2249A>T|p.Glu750Val|2249/13218|2249/13218|750/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1709A>T|p.Glu570Val|1709/1914|1709/1914|570/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1709A>T|p.Glu570Val|1709/1914|1709/1914|570/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-206A>T|||||206|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-206A>T|||||206|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1709A>T|||||1709|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1709A>T|||||1709|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:343:1:16:0,-1.41032,-29.6276

-NC_045512.2	2665	.	T	C	1.5452E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.8489;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=411;RO=11;RPL=0;RPP=5.18177;RPPR=3.20771;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=3.20771;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2400T>C|p.Cys800Cys|2400/21291|2400/21291|800/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2400T>C|p.Cys800Cys|2400/13218|2400/13218|800/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1860T>C|p.Cys620Cys|1860/1914|1860/1914|620/637||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1860T>C|p.Cys620Cys|1860/1914|1860/1914|620/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-55T>C|||||55|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-55T>C|||||55|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1860T>C|||||1860|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1860T>C|||||1860|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:12:11,1:11:411:1:26:0,-1.01253,-34.735

-NC_045512.2	2888	.	G	C	3.41564E-7	.	AB=0.107143;ABP=40.5458;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=9.52472;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=56;MQMR=60;NS=1;NUMALT=1;ODDS=16.3583;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=118;QR=961;RO=25;RPL=0;RPP=9.52472;RPPR=17.6895;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=19;SRP=17.6895;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2623G>C|p.Val875Leu|2623/21291|2623/21291|875/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2623G>C|p.Val875Leu|2623/13218|2623/13218|875/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.169G>C|p.Val57Leu|169/5835|169/5835|57/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.169G>C|p.Val57Leu|169/5835|169/5835|57/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2083G>C|||||2083|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2083G>C|||||2083|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*169G>C|||||169|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*169G>C|||||169|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:28:25,3:25:961:3:118:-2.51845,0,-78.3749

-NC_045512.2	2895	.	ATG	AG	2.49976E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=29;DPB=28.6667;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5714;NS=1;NUMALT=1;ODDS=35.6936;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1020;RO=28;RPL=1;RPP=5.18177;RPPR=28.1373;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=28.1373;SRR=5;TYPE=del;ANN=AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2631delT|p.Asp877fs|2631/21291|2631/21291|877/7096||,AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2631delT|p.Asp877fs|2631/13218|2631/13218|877/4405||,AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.177delT|p.Asp59fs|177/5835|177/5835|59/1944||WARNING_TRANSCRIPT_NO_START_CODON,AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.177delT|p.Asp59fs|177/5835|177/5835|59/1944||WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2091delT|||||2091|WARNING_TRANSCRIPT_NO_STOP_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2091delT|||||2091|WARNING_TRANSCRIPT_NO_STOP_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*177delT|||||177|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*177delT|||||177|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:29:28,1:28:1020:1:34:0,-5.33096,-88.6724

-NC_045512.2	2970	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=90.0666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7273;NS=1;NUMALT=1;ODDS=62.2679;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1691;RO=44;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=3.20771;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2705T>C|p.Met902Thr|2705/21291|2705/21291|902/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2705T>C|p.Met902Thr|2705/13218|2705/13218|902/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.251T>C|p.Met84Thr|251/5835|251/5835|84/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.251T>C|p.Met84Thr|251/5835|251/5835|84/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2165T>C|||||2165|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2165T>C|||||2165|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*251T>C|||||251|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*251T>C|||||251|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1691:1:13:0,-12.2464,-151.098

-NC_045512.2	3001	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=90.0666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7273;NS=1;NUMALT=1;ODDS=61.5771;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1620;RO=44;RPL=1;RPP=5.18177;RPPR=3.20771;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=3.0103;SRR=22;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2736T>A|p.Gly912Gly|2736/21291|2736/21291|912/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2736T>A|p.Gly912Gly|2736/13218|2736/13218|912/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.282T>A|p.Gly94Gly|282/5835|282/5835|94/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.282T>A|p.Gly94Gly|282/5835|282/5835|94/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2196T>A|||||2196|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2196T>A|||||2196|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*282T>A|||||282|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*282T>A|||||282|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1620:1:16:0,-11.9464,-144.412

-NC_045512.2	3037	.	C	T	1417.61	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=45;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=100.727;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=59.7333;MQMR=0;NS=1;NUMALT=1;ODDS=66.9884;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1744;QR=0;RO=0;RPL=23;RPP=3.05855;RPPR=0;RPR=22;RUN=1;SAF=23;SAP=3.05855;SAR=22;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2772C>T|p.Phe924Phe|2772/13218|2772/13218|924/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.318C>T|p.Phe106Phe|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.318C>T|p.Phe106Phe|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2232C>T|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2232C>T|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*318C>T|||||318|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*318C>T|||||318|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:45:0,45:0:0:45:1744:-157.171,-13.5464,0

-NC_045512.2	3067	.	T	C	394.855	.	AB=0.422222;ABP=5.37479;AC=1;AF=0.5;AN=2;AO=19;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=44.2683;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5385;NS=1;NUMALT=1;ODDS=90.9187;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=701;QR=912;RO=26;RPL=10;RPP=3.12459;RPPR=3.0103;RPR=9;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2802T>C|p.Gly934Gly|2802/21291|2802/21291|934/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2802T>C|p.Gly934Gly|2802/13218|2802/13218|934/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.348T>C|p.Gly116Gly|348/5835|348/5835|116/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.348T>C|p.Gly116Gly|348/5835|348/5835|116/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2262T>C|||||2262|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2262T>C|||||2262|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*348T>C|||||348|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*348T>C|||||348|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:45:26,19:26:912:19:701:-49.8723,0,-68.8154

-NC_045512.2	3103	.	A	G	1.89084E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=42.4916;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.8288;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=857;RO=22;RPL=1;RPP=5.18177;RPPR=50.7827;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=42.4916;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2838A>G|p.Gln946Gln|2838/21291|2838/21291|946/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2838A>G|p.Gln946Gln|2838/13218|2838/13218|946/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.384A>G|p.Gln128Gln|384/5835|384/5835|128/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.384A>G|p.Gln128Gln|384/5835|384/5835|128/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2298A>G|||||2298|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2298A>G|||||2298|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*384A>G|||||384|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*384A>G|||||384|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:857:1:20:0,-4.92373,-75.4519

-NC_045512.2	3109	.	G	T	1.40218E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=42.4916;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.4617;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=855;RO=22;RPL=1;RPP=5.18177;RPPR=50.7827;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=42.4916;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2844G>T|p.Glu948Asp|2844/21291|2844/21291|948/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2844G>T|p.Glu948Asp|2844/13218|2844/13218|948/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.390G>T|p.Glu130Asp|390/5835|390/5835|130/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.390G>T|p.Glu130Asp|390/5835|390/5835|130/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2304G>T|||||2304|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2304G>T|||||2304|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*390G>T|||||390|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*390G>T|||||390|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:855:1:39:0,-3.02713,-73.3755

-NC_045512.2	3147	.	A	G	1.68157E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=39.5244;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=1153;RO=31;RPL=0;RPP=5.18177;RPPR=14.8483;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=14.8483;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2882A>G|p.Glu961Gly|2882/21291|2882/21291|961/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2882A>G|p.Glu961Gly|2882/13218|2882/13218|961/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.428A>G|p.Glu143Gly|428/5835|428/5835|143/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.428A>G|p.Glu143Gly|428/5835|428/5835|143/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2342A>G|||||2342|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2342A>G|||||2342|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*428A>G|||||428|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*428A>G|||||428|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1153:1:35:0,-6.13433,-100.558

-NC_045512.2	3149	.	T	A	1.55952E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.2941;NS=1;NUMALT=1;ODDS=38.2282;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=64;QR=1247;RO=34;RPL=0;RPP=7.35324;RPPR=9.39698;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=12;SRP=9.39698;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2884T>A|p.Phe962Ile|2884/21291|2884/21291|962/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2884T>A|p.Phe962Ile|2884/13218|2884/13218|962/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.430T>A|p.Phe144Ile|430/5835|430/5835|144/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.430T>A|p.Phe144Ile|430/5835|430/5835|144/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2344T>A|||||2344|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2344T>A|||||2344|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*430T>A|||||430|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*430T>A|||||430|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,2:34:1247:2:64:0,-4.75839,-106.419

-NC_045512.2	3178	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4419;NS=1;NUMALT=1;ODDS=54.9252;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1666;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0608;SRR=21;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2913T>C|p.Pro971Pro|2913/21291|2913/21291|971/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2913T>C|p.Pro971Pro|2913/13218|2913/13218|971/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.459T>C|p.Pro153Pro|459/5835|459/5835|153/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.459T>C|p.Pro153Pro|459/5835|459/5835|153/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2373T>C|||||2373|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2373T>C|||||2373|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*459T>C|||||459|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*459T>C|||||459|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1666:1:39:0,-9.34875,-146.217

-NC_045512.2	3195	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4419;NS=1;NUMALT=1;ODDS=55.1538;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1636;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0608;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2930A>G|p.Glu977Gly|2930/21291|2930/21291|977/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2930A>G|p.Glu977Gly|2930/13218|2930/13218|977/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.476A>G|p.Glu159Gly|476/5835|476/5835|159/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.476A>G|p.Glu159Gly|476/5835|476/5835|159/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2390A>G|||||2390|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2390A>G|||||2390|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*476A>G|||||476|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*476A>G|||||476|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1636:1:38:0,-9.44805,-143.627

-NC_045512.2	3196	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4419;NS=1;NUMALT=1;ODDS=55.3828;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1645;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0608;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2931A>G|p.Glu977Glu|2931/21291|2931/21291|977/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2931A>G|p.Glu977Glu|2931/13218|2931/13218|977/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.477A>G|p.Glu159Glu|477/5835|477/5835|159/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.477A>G|p.Glu159Glu|477/5835|477/5835|159/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2391A>G|||||2391|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2391A>G|||||2391|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*477A>G|||||477|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*477A>G|||||477|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1645:1:37:0,-9.54749,-144.542

-NC_045512.2	3309	.	A	C	187.554	.	AB=0.266667;ABP=24.2907;AC=1;AF=0.5;AN=2;AO=12;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=29.068;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=58;MQMR=60;NS=1;NUMALT=1;ODDS=43.1859;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=467;QR=1285;RO=33;RPL=6;RPP=3.0103;RPPR=3.0761;RPR=6;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3044A>C|p.Glu1015Ala|3044/21291|3044/21291|1015/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3044A>C|p.Glu1015Ala|3044/13218|3044/13218|1015/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.590A>C|p.Glu197Ala|590/5835|590/5835|197/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.590A>C|p.Glu197Ala|590/5835|590/5835|197/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2504A>C|||||2504|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2504A>C|||||2504|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*590A>C|||||590|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*590A>C|||||590|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:45:33,12:33:1285:12:467:-28.7487,0,-102.392

-NC_045512.2	3394	.	A	G	2.34909E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=7.35324;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.3333;NS=1;NUMALT=1;ODDS=38.8501;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=1379;RO=36;RPL=1;RPP=3.0103;RPPR=6.8707;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=6.8707;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3129A>G|p.Ala1043Ala|3129/21291|3129/21291|1043/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3129A>G|p.Ala1043Ala|3129/13218|3129/13218|1043/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.675A>G|p.Ala225Ala|675/5835|675/5835|225/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.675A>G|p.Ala225Ala|675/5835|675/5835|225/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2589A>G|||||2589|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2589A>G|||||2589|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*675A>G|||||675|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*675A>G|||||675|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:36,2:36:1379:2:67:0,-5.07609,-117.952

-NC_045512.2	3400	.	T	G	4.41335E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.4822;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1164;RO=30;RPL=0;RPP=5.18177;RPPR=17.1973;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=17.1973;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3135T>G|p.Ile1045Met|3135/21291|3135/21291|1045/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3135T>G|p.Ile1045Met|3135/13218|3135/13218|1045/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.681T>G|p.Ile227Met|681/5835|681/5835|227/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.681T>G|p.Ile227Met|681/5835|681/5835|227/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2595T>G|||||2595|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2595T>G|||||2595|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*681T>G|||||681|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*681T>G|||||681|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1164:1:38:0,-5.53466,-101.261

-NC_045512.2	3517	.	A	G	4.49473E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=7.35324;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.5984;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1104;RO=29;RPL=1;RPP=3.0103;RPPR=19.8579;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=19.8579;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3252A>G|p.Gln1084Gln|3252/21291|3252/21291|1084/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3252A>G|p.Gln1084Gln|3252/13218|3252/13218|1084/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.798A>G|p.Gln266Gln|798/5835|798/5835|266/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.798A>G|p.Gln266Gln|798/5835|798/5835|266/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2712A>G|||||2712|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2712A>G|||||2712|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*798A>G|||||798|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*798A>G|||||798|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:29,2:29:1104:2:76:0,-2.11726,-92.4527

-NC_045512.2	3587	.	C	T	0.00415304	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.95199;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=266;RO=7;RPL=0;RPP=5.18177;RPPR=3.32051;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=18.2106;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3322C>T|p.His1108Tyr|3322/21291|3322/21291|1108/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3322C>T|p.His1108Tyr|3322/13218|3322/13218|1108/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.868C>T|p.His290Tyr|868/5835|868/5835|290/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.868C>T|p.His290Tyr|868/5835|868/5835|290/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4968C>T|||||4968|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4968C>T|||||4968|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2782C>T|||||2782|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2782C>T|||||2782|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*868C>T|||||868|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*868C>T|||||868|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:266:1:38:-1.38903,0,-21.8943

-NC_045512.2	3624	.	C	T	0.00154508	.	AB=0.125;ABP=22.5536;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=7.35324;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.94106;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=528;RO=14;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3359C>T|p.Pro1120Leu|3359/21291|3359/21291|1120/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3359C>T|p.Pro1120Leu|3359/13218|3359/13218|1120/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.905C>T|p.Pro302Leu|905/5835|905/5835|302/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.905C>T|p.Pro302Leu|905/5835|905/5835|302/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4931C>T|||||4931|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4931C>T|||||4931|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2819C>T|||||2819|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2819C>T|||||2819|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*905C>T|||||905|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*905C>T|||||905|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:16:14,2:14:528:2:77:-2.49266,0,-43.0472

-NC_045512.2	3717	.	C	T	4.0798E-4	.	AB=0.1;ABP=16.9077;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.2728;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=345;RO=9;RPL=0;RPP=5.18177;RPPR=9.04217;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3452C>T|p.Ala1151Val|3452/21291|3452/21291|1151/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3452C>T|p.Ala1151Val|3452/13218|3452/13218|1151/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.998C>T|p.Ala333Val|998/5835|998/5835|333/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.998C>T|p.Ala333Val|998/5835|998/5835|333/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4838C>T|||||4838|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4838C>T|||||4838|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2912C>T|||||2912|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2912C>T|||||2912|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*998C>T|||||998|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*998C>T|||||998|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:9,1:9:345:1:39:-0.886264,0,-28.3982

-NC_045512.2	4051	.	TCT	TT	1.11859	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1M1D1M;DP=3;DPB=2.66667;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.23032;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=78;RO=2;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=0;SRP=7.35324;SRR=2;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3787delC|p.Leu1263fs|3787/21291|3787/21291|1263/7096||,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3787delC|p.Leu1263fs|3787/13218|3787/13218|1263/4405||,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1333delC|p.Leu445fs|1333/5835|1333/5835|445/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1333delC|p.Leu445fs|1333/5835|1333/5835|445/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4503delC|||||4503|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4503delC|||||4503|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3247delC|||||3247|WARNING_TRANSCRIPT_NO_STOP_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3247delC|||||3247|WARNING_TRANSCRIPT_NO_STOP_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1333delC|||||1333|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1333delC|||||1333|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:78:1:37:-2.79474,0,-6.50038

-NC_045512.2	4229	.	ACAGACAA	TAAGTCAT	1.18584E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X2M1X2M1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=8;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=36.7156;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=987;RO=26;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=complex;ANN=TAAGTCAT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3964_3971delACAGACAAinsTAAGTCAT|p.ThrAspAsn1322*|3964/21291|3964/21291|1322/7096||,TAAGTCAT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3964_3971delACAGACAAinsTAAGTCAT|p.ThrAspAsn1322*|3964/13218|3964/13218|1322/4405||,TAAGTCAT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1510_1517delACAGACAAinsTAAGTCAT|p.ThrAspAsn504*|1510/5835|1510/5835|504/1944||WARNING_TRANSCRIPT_NO_START_CODON,TAAGTCAT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1510_1517delACAGACAAinsTAAGTCAT|p.ThrAspAsn504*|1510/5835|1510/5835|504/1944||WARNING_TRANSCRIPT_NO_START_CODON,TAAGTCAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4326_-4319delACAGACAAinsTAAGTCAT|||||4326|WARNING_TRANSCRIPT_NO_START_CODON,TAAGTCAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4326_-4319delACAGACAAinsTAAGTCAT|||||4326|WARNING_TRANSCRIPT_NO_START_CODON,TAAGTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3424_*3431delACAGACAAinsTAAGTCAT|||||3424|WARNING_TRANSCRIPT_NO_STOP_CODON,TAAGTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3424_*3431delACAGACAAinsTAAGTCAT|||||3424|WARNING_TRANSCRIPT_NO_STOP_CODON,TAAGTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1510_*1517delACAGACAAinsTAAGTCAT|||||1510|WARNING_TRANSCRIPT_NO_START_CODON,TAAGTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1510_*1517delACAGACAAinsTAAGTCAT|||||1510|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:987:1:19:0,-6.34583,-87.3601

-NC_045512.2	4245	.	CCACTTACCCGGGTC	ACATTTGCCAAGGTT	1.18584E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X2M1X2M2X3M1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=15;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=36.7156;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=972;RO=26;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=complex;ANN=ACATTTGCCAAGGTT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3980_3994delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|p.ThrThrTyrProGlyGln1327*|3980/21291|3980/21291|1327/7096||,ACATTTGCCAAGGTT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3980_3994delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|p.ThrThrTyrProGlyGln1327*|3980/13218|3980/13218|1327/4405||,ACATTTGCCAAGGTT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1526_1540delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|p.ThrThrTyrProGlyGln509*|1526/5835|1526/5835|509/1944||WARNING_TRANSCRIPT_NO_START_CODON,ACATTTGCCAAGGTT|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1526_1540delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|p.ThrThrTyrProGlyGln509*|1526/5835|1526/5835|509/1944||WARNING_TRANSCRIPT_NO_START_CODON,ACATTTGCCAAGGTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4310_-4296delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|||||4310|WARNING_TRANSCRIPT_NO_START_CODON,ACATTTGCCAAGGTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4310_-4296delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|||||4310|WARNING_TRANSCRIPT_NO_START_CODON,ACATTTGCCAAGGTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3440_*3454delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|||||3440|WARNING_TRANSCRIPT_NO_STOP_CODON,ACATTTGCCAAGGTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3440_*3454delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|||||3440|WARNING_TRANSCRIPT_NO_STOP_CODON,ACATTTGCCAAGGTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1526_*1540delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|||||1526|WARNING_TRANSCRIPT_NO_START_CODON,ACATTTGCCAAGGTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1526_*1540delCCACTTACCCGGGTCinsACATTTGCCAAGGTT|||||1526|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:972:1:19:0,-6.34583,-86.0117

-NC_045512.2	4291	.	A	T	5.96525E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=7.35324;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.56;NS=1;NUMALT=1;ODDS=31.9472;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=933;RO=25;RPL=1;RPP=3.0103;RPPR=3.09716;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=12;SRP=3.09716;SRR=13;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4026A>T|p.Ala1342Ala|4026/21291|4026/21291|1342/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4026A>T|p.Ala1342Ala|4026/13218|4026/13218|1342/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1572A>T|p.Ala524Ala|1572/5835|1572/5835|524/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1572A>T|p.Ala524Ala|1572/5835|1572/5835|524/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4264A>T|||||4264|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4264A>T|||||4264|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3486A>T|||||3486|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3486A>T|||||3486|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1572A>T|||||1572|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1572A>T|||||1572|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:25,2:25:933:2:32:0,-5.08785,-81.1692

-NC_045512.2	4293	.	AGA	TGT	1.18584E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=3;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=36.7156;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=985;RO=26;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=complex;ANN=TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4028_4030delAGAinsTGT|p.LysThr1343MetSer|4028/21291|4028/21291|1343/7096||,TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4028_4030delAGAinsTGT|p.LysThr1343MetSer|4028/13218|4028/13218|1343/4405||,TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1574_1576delAGAinsTGT|p.LysThr525MetSer|1574/5835|1574/5835|525/1944||WARNING_TRANSCRIPT_NO_START_CODON,TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1574_1576delAGAinsTGT|p.LysThr525MetSer|1574/5835|1574/5835|525/1944||WARNING_TRANSCRIPT_NO_START_CODON,TGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4262_-4260delAGAinsTGT|||||4262|WARNING_TRANSCRIPT_NO_START_CODON,TGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4262_-4260delAGAinsTGT|||||4262|WARNING_TRANSCRIPT_NO_START_CODON,TGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3488_*3490delAGAinsTGT|||||3488|WARNING_TRANSCRIPT_NO_STOP_CODON,TGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3488_*3490delAGAinsTGT|||||3488|WARNING_TRANSCRIPT_NO_STOP_CODON,TGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1574_*1576delAGAinsTGT|||||1574|WARNING_TRANSCRIPT_NO_START_CODON,TGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1574_*1576delAGAinsTGT|||||1574|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:985:1:19:0,-6.34583,-87.1779

-NC_045512.2	4300	.	G	T	1.27929E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=3.09072;GTI=0;LEN=1;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=38.6282;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=984;RO=27;RPL=0;RPP=5.18177;RPPR=38.4777;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4035G>T|p.Val1345Val|4035/21291|4035/21291|1345/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4035G>T|p.Val1345Val|4035/13218|4035/13218|1345/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1581G>T|p.Val527Val|1581/5835|1581/5835|527/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1581G>T|p.Val527Val|1581/5835|1581/5835|527/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4255G>T|||||4255|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4255G>T|||||4255|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3495G>T|||||3495|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3495G>T|||||3495|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1581G>T|||||1581|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1581G>T|||||1581|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:984:1:16:0,-6.89124,-87.321

-NC_045512.2	4322	.	TTTTA	ATTTT	1.22418E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=27.4756;GTI=0;LEN=5;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=21.9896;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=576;RO=15;RPL=0;RPP=5.18177;RPPR=14.7363;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=complex;ANN=ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4057_4061delTTTTAinsATTTT|p.PheTyr1353IlePhe|4057/21291|4057/21291|1353/7096||,ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4057_4061delTTTTAinsATTTT|p.PheTyr1353IlePhe|4057/13218|4057/13218|1353/4405||,ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1603_1607delTTTTAinsATTTT|p.PheTyr535IlePhe|1603/5835|1603/5835|535/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1603_1607delTTTTAinsATTTT|p.PheTyr535IlePhe|1603/5835|1603/5835|535/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4233_-4229delTTTTAinsATTTT|||||4233|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4233_-4229delTTTTAinsATTTT|||||4233|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3517_*3521delTTTTAinsATTTT|||||3517|WARNING_TRANSCRIPT_NO_STOP_CODON,ATTTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3517_*3521delTTTTAinsATTTT|||||3517|WARNING_TRANSCRIPT_NO_STOP_CODON,ATTTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1603_*1607delTTTTAinsATTTT|||||1603|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1603_*1607delTTTTAinsATTTT|||||1603|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:576:1:19:0,-3.0345,-50.3991

-NC_045512.2	4341	.	T	A	8.47806E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=22.3569;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=557;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4076T>A|p.Ile1359Asn|4076/21291|4076/21291|1359/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4076T>A|p.Ile1359Asn|4076/13218|4076/13218|1359/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1622T>A|p.Ile541Asn|1622/5835|1622/5835|541/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1622T>A|p.Ile541Asn|1622/5835|1622/5835|541/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4214T>A|||||4214|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4214T>A|||||4214|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3536T>A|||||3536|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3536T>A|||||3536|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1622T>A|||||1622|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1622T>A|||||1622|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:557:1:17:0,-3.19405,-48.8384

-NC_045512.2	4358	.	CA	TT	8.47806E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=2;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=22.3569;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=578;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4093_4094delCAinsTT|p.Gln1365Leu|4093/21291|4093/21291|1365/7096||,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4093_4094delCAinsTT|p.Gln1365Leu|4093/13218|4093/13218|1365/4405||,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1639_1640delCAinsTT|p.Gln547Leu|1639/5835|1639/5835|547/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1639_1640delCAinsTT|p.Gln547Leu|1639/5835|1639/5835|547/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4197_-4196delCAinsTT|||||4197|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4197_-4196delCAinsTT|||||4197|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3553_*3554delCAinsTT|||||3553|WARNING_TRANSCRIPT_NO_STOP_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3553_*3554delCAinsTT|||||3553|WARNING_TRANSCRIPT_NO_STOP_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1639_*1640delCAinsTT|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1639_*1640delCAinsTT|||||1639|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:578:1:17:0,-3.19405,-50.7394

-NC_045512.2	4370	.	G	A	8.47806E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=22.3569;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=574;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4105G>A|p.Gly1369Arg|4105/21291|4105/21291|1369/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4105G>A|p.Gly1369Arg|4105/13218|4105/13218|1369/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1651G>A|p.Gly551Arg|1651/5835|1651/5835|551/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1651G>A|p.Gly551Arg|1651/5835|1651/5835|551/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4185G>A|||||4185|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4185G>A|||||4185|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3565G>A|||||3565|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3565G>A|||||3565|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1651G>A|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1651G>A|||||1651|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:574:1:17:0,-3.19405,-50.3779

-NC_045512.2	4371	.	G	A	2.02215E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=57.6;NS=1;NUMALT=1;ODDS=21.4877;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=553;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4106G>A|p.Gly1369Glu|4106/21291|4106/21291|1369/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4106G>A|p.Gly1369Glu|4106/13218|4106/13218|1369/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1652G>A|p.Gly551Glu|1652/5835|1652/5835|551/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1652G>A|p.Gly551Glu|1652/5835|1652/5835|551/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4184G>A|||||4184|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4184G>A|||||4184|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3566G>A|||||3566|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3566G>A|||||3566|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1652G>A|||||1652|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1652G>A|||||1652|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:553:1:20:0,-2.81652,-48.0293

-NC_045512.2	4391	.	CGAG	AGAA	1.45063E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=4;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=21.8198;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=557;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=complex;ANN=AGAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4126_4129delCGAGinsAGAA|p.Glu1377Lys|4126/21291|4126/21291|1376/7096||,AGAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4126_4129delCGAGinsAGAA|p.Glu1377Lys|4126/13218|4126/13218|1376/4405||,AGAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1672_1675delCGAGinsAGAA|p.Glu559Lys|1672/5835|1672/5835|558/1944||WARNING_TRANSCRIPT_NO_START_CODON,AGAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1672_1675delCGAGinsAGAA|p.Glu559Lys|1672/5835|1672/5835|558/1944||WARNING_TRANSCRIPT_NO_START_CODON,AGAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4164_-4161delCGAGinsAGAA|||||4164|WARNING_TRANSCRIPT_NO_START_CODON,AGAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4164_-4161delCGAGinsAGAA|||||4164|WARNING_TRANSCRIPT_NO_START_CODON,AGAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3586_*3589delCGAGinsAGAA|||||3586|WARNING_TRANSCRIPT_NO_STOP_CODON,AGAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3586_*3589delCGAGinsAGAA|||||3586|WARNING_TRANSCRIPT_NO_STOP_CODON,AGAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1672_*1675delCGAGinsAGAA|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,AGAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1672_*1675delCGAGinsAGAA|||||1672|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:557:1:20:0,-2.96078,-48.6123

-NC_045512.2	4412	.	GAAGAAAC	GAGAAAC	1.00852E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D6M;DP=16;DPB=15.875;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=57.6;NS=1;NUMALT=1;ODDS=17.5782;PAIRED=1;PAIREDR=0.933333;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=513;RO=15;RPL=1;RPP=5.18177;RPPR=20.5268;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=20.5268;SRR=13;TYPE=del;ANN=GAGAAAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4149delA|p.Glu1384fs|4149/21291|4149/21291|1383/7096||,GAGAAAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4149delA|p.Glu1384fs|4149/13218|4149/13218|1383/4405||,GAGAAAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1695delA|p.Glu566fs|1695/5835|1695/5835|565/1944||WARNING_TRANSCRIPT_NO_START_CODON,GAGAAAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1695delA|p.Glu566fs|1695/5835|1695/5835|565/1944||WARNING_TRANSCRIPT_NO_START_CODON,GAGAAAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4141delA|||||4141|WARNING_TRANSCRIPT_NO_START_CODON,GAGAAAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4141delA|||||4141|WARNING_TRANSCRIPT_NO_START_CODON,GAGAAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3609delA|||||3609|WARNING_TRANSCRIPT_NO_STOP_CODON,GAGAAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3609delA|||||3609|WARNING_TRANSCRIPT_NO_STOP_CODON,GAGAAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1695delA|||||1695|WARNING_TRANSCRIPT_NO_START_CODON,GAGAAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1695delA|||||1695|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:513:1:37:0,-1.11865,-42.421

-NC_045512.2	4423	.	C	A	5.32009E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=14.5915;GTI=0;LEN=1;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=18.2177;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=414;RO=12;RPL=1;RPP=5.18177;RPPR=29.068;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=14.5915;SRR=10;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4158C>A|p.Arg1386Arg|4158/21291|4158/21291|1386/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4158C>A|p.Arg1386Arg|4158/13218|4158/13218|1386/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1704C>A|p.Arg568Arg|1704/5835|1704/5835|568/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1704C>A|p.Arg568Arg|1704/5835|1704/5835|568/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4132C>A|||||4132|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4132C>A|||||4132|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3618C>A|||||3618|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3618C>A|||||3618|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1704C>A|||||1704|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1704C>A|||||1704|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:414:1:18:0,-2.20933,-35.8856

-NC_045512.2	4445	.	G	C	4.02279E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=24;MQMR=60;NS=1;NUMALT=1;ODDS=9.28687;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=164;RO=5;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4180G>C|p.Glu1394Gln|4180/21291|4180/21291|1394/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4180G>C|p.Glu1394Gln|4180/13218|4180/13218|1394/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1726G>C|p.Glu576Gln|1726/5835|1726/5835|576/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1726G>C|p.Glu576Gln|1726/5835|1726/5835|576/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4110G>C|||||4110|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4110G>C|||||4110|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3640G>C|||||3640|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3640G>C|||||3640|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1726G>C|||||1726|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1726G>C|||||1726|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:164:1:18:0,-0.102119,-13.3747

-NC_045512.2	4479	.	A	T	0.00213012	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.6199;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=112;RO=3;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=3.73412;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4214A>T|p.Lys1405Ile|4214/21291|4214/21291|1405/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4214A>T|p.Lys1405Ile|4214/13218|4214/13218|1405/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1760A>T|p.Lys587Ile|1760/5835|1760/5835|587/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1760A>T|p.Lys587Ile|1760/5835|1760/5835|587/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4076A>T|||||4076|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4076A>T|||||4076|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3674A>T|||||3674|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3674A>T|||||3674|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1760A>T|||||1760|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1760A>T|||||1760|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:112:1:14:-0.19587,0,-9.24218

-NC_045512.2	4758	.	A	G	0.0115511	.	AB=0.142857;ABP=10.7656;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.9282;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=233;RO=6;RPL=0;RPP=5.18177;RPPR=16.0391;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=16.0391;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4493A>G|p.Glu1498Gly|4493/21291|4493/21291|1498/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4493A>G|p.Glu1498Gly|4493/13218|4493/13218|1498/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2039A>G|p.Glu680Gly|2039/5835|2039/5835|680/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2039A>G|p.Glu680Gly|2039/5835|2039/5835|680/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3797A>G|||||3797|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3797A>G|||||3797|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3953A>G|||||3953|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3953A>G|||||3953|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2039A>G|||||2039|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2039A>G|||||2039|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:6,1:6:233:1:37:-1.59062,0,-19.2329

-NC_045512.2	4913	.	G	T	6.31765	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.18881;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=195;RO=5;RPL=2;RPP=7.35324;RPPR=13.8677;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=13.8677;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4648G>T|p.Val1550Phe|4648/21291|4648/21291|1550/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4648G>T|p.Val1550Phe|4648/13218|4648/13218|1550/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2194G>T|p.Val732Phe|2194/5835|2194/5835|732/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2194G>T|p.Val732Phe|2194/5835|2194/5835|732/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3642G>T|||||3642|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3642G>T|||||3642|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4108G>T|||||4108|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4108G>T|||||4108|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2194G>T|||||2194|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2194G>T|||||2194|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:5,2:5:195:2:76:-5.10746,0,-15.817

-NC_045512.2	4960	.	G	T	1.77522E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=498;RO=13;RPL=0;RPP=5.18177;RPPR=3.17734;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4695G>T|p.Val1565Val|4695/21291|4695/21291|1565/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4695G>T|p.Val1565Val|4695/13218|4695/13218|1565/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2241G>T|p.Val747Val|2241/5835|2241/5835|747/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2241G>T|p.Val747Val|2241/5835|2241/5835|747/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3595G>T|||||3595|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3595G>T|||||3595|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4155G>T|||||4155|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4155G>T|||||4155|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2241G>T|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2241G>T|||||2241|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:498:1:38:0,-0.417151,-41.3709

-NC_045512.2	4999	.	C	T	2.23124E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.4815;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=499;RO=13;RPL=0;RPP=5.18177;RPPR=3.17734;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4734C>T|p.Asn1578Asn|4734/21291|4734/21291|1578/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4734C>T|p.Asn1578Asn|4734/13218|4734/13218|1578/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2280C>T|p.Asn760Asn|2280/5835|2280/5835|760/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2280C>T|p.Asn760Asn|2280/5835|2280/5835|760/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3556C>T|||||3556|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3556C>T|||||3556|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4194C>T|||||4194|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4194C>T|||||4194|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2280C>T|||||2280|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2280C>T|||||2280|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:499:1:39:0,-0.317855,-41.3617

-NC_045512.2	5259	.	C	A	1.23084E-4	.	AB=0.133333;ABP=20.5268;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=7.35324;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.4712;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=466;RO=13;RPL=0;RPP=7.35324;RPPR=3.17734;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4994C>A|p.Thr1665Asn|4994/21291|4994/21291|1665/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4994C>A|p.Thr1665Asn|4994/13218|4994/13218|1665/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2540C>A|p.Thr847Asn|2540/5835|2540/5835|847/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2540C>A|p.Thr847Asn|2540/5835|2540/5835|847/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3296C>A|||||3296|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3296C>A|||||3296|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4796C>A|||||4796|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4796C>A|||||4796|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4454C>A|||||4454|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4454C>A|||||4454|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2540C>A|||||2540|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2540C>A|||||2540|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:15:13,2:13:466:2:66:-1.75286,0,-37.7564

-NC_045512.2	5421	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1641;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5156A>G|p.Asn1719Ser|5156/21291|5156/21291|1719/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5156A>G|p.Asn1719Ser|5156/13218|5156/13218|1719/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2702A>G|p.Asn901Ser|2702/5835|2702/5835|901/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2702A>G|p.Asn901Ser|2702/5835|2702/5835|901/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3134A>G|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3134A>G|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4634A>G|||||4634|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4634A>G|||||4634|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4616A>G|||||4616|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4616A>G|||||4616|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2702A>G|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2702A>G|||||2702|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1641:1:17:0,-11.5453,-146.247

-NC_045512.2	5487	.	T	A	6.13276E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.4435;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1664;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5222T>A|p.Leu1741*|5222/21291|5222/21291|1741/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5222T>A|p.Leu1741*|5222/13218|5222/13218|1741/4405||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2768T>A|p.Leu923*|2768/5835|2768/5835|923/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2768T>A|p.Leu923*|2768/5835|2768/5835|923/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3068T>A|||||3068|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3068T>A|||||3068|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4568T>A|||||4568|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4568T>A|||||4568|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4682T>A|||||4682|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4682T>A|||||4682|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2768T>A|||||2768|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2768T>A|||||2768|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1664:1:15:0,-11.7453,-148.52

-NC_045512.2	5497	.	C	A	6.13276E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.4435;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1661;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5232C>A|p.Cys1744*|5232/21291|5232/21291|1744/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5232C>A|p.Cys1744*|5232/13218|5232/13218|1744/4405||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2778C>A|p.Cys926*|2778/5835|2778/5835|926/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2778C>A|p.Cys926*|2778/5835|2778/5835|926/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3058C>A|||||3058|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3058C>A|||||3058|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4558C>A|||||4558|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4558C>A|||||4558|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4692C>A|||||4692|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4692C>A|||||4692|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2778C>A|||||2778|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2778C>A|||||2778|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1661:1:15:0,-11.7453,-148.251

-NC_045512.2	5498	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.1343;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1622;RO=43;RPL=1;RPP=5.18177;RPPR=3.0608;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5233A>G|p.Lys1745Glu|5233/21291|5233/21291|1745/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5233A>G|p.Lys1745Glu|5233/13218|5233/13218|1745/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2779A>G|p.Lys927Glu|2779/5835|2779/5835|927/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2779A>G|p.Lys927Glu|2779/5835|2779/5835|927/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3057A>G|||||3057|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3057A>G|||||3057|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4557A>G|||||4557|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4557A>G|||||4557|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4693A>G|||||4693|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4693A>G|||||4693|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2779A>G|||||2779|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2779A>G|||||2779|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1622:1:12:0,-12.0453,-145.039

-NC_045512.2	5943	.	A	G	1.06969E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.8219;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=592;RO=16;RPL=1;RPP=5.18177;RPPR=3.55317;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.55317;SRR=7;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5678A>G|p.Asp1893Gly|5678/21291|5678/21291|1893/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5678A>G|p.Asp1893Gly|5678/13218|5678/13218|1893/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3224A>G|p.Asp1075Gly|3224/5835|3224/5835|1075/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3224A>G|p.Asp1075Gly|3224/5835|3224/5835|1075/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2612A>G|||||2612|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2612A>G|||||2612|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4112A>G|||||4112|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4112A>G|||||4112|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3224A>G|||||3224|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3224A>G|||||3224|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:592:1:33:0,-1.81837,-50.3115

-NC_045512.2	6181	.	TAAACACT	TAACACT	2.92095E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D6M;DP=24;DPB=23.875;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.0341;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=867;RO=23;RPL=0;RPP=5.18177;RPPR=5.3706;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=5.3706;SRR=9;TYPE=del;ANN=TAACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5919delA|p.Lys1973fs|5919/21291|5919/21291|1973/7096||,TAACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5919delA|p.Lys1973fs|5919/13218|5919/13218|1973/4405||,TAACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3465delA|p.Lys1155fs|3465/5835|3465/5835|1155/1944||WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3465delA|p.Lys1155fs|3465/5835|3465/5835|1155/1944||WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2371delA|||||2371|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2371delA|||||2371|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3871delA|||||3871|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3871delA|||||3871|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4789delA|||||4789|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4789delA|||||4789|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3465delA|||||3465|WARNING_TRANSCRIPT_NO_START_CODON,TAACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3465delA|||||3465|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:867:1:38:0,-3.42745,-74.5559

-NC_045512.2	6253	.	T	C	3.65676E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8055;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=886;RO=23;RPL=0;RPP=5.18177;RPPR=5.3706;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=5.3706;SRR=9;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5988T>C|p.Asn1996Asn|5988/21291|5988/21291|1996/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5988T>C|p.Asn1996Asn|5988/13218|5988/13218|1996/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3534T>C|p.Asn1178Asn|3534/5835|3534/5835|1178/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3534T>C|p.Asn1178Asn|3534/5835|3534/5835|1178/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2302T>C|||||2302|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2302T>C|||||2302|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3802T>C|||||3802|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3802T>C|||||3802|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4720T>C|||||4720|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4720T>C|||||4720|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3534T>C|||||3534|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3534T>C|||||3534|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:886:1:39:0,-3.32816,-76.1641

-NC_045512.2	6286	.	C	T	337.596	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=33.4109;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.7988;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=545;QR=39;RO=1;RPL=0;RPP=33.4109;RPPR=5.18177;RPR=14;RUN=1;SAF=14;SAP=33.4109;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6021C>T|p.Thr2007Thr|6021/21291|6021/21291|2007/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6021C>T|p.Thr2007Thr|6021/13218|6021/13218|2007/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3567C>T|p.Thr1189Thr|3567/5835|3567/5835|1189/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3567C>T|p.Thr1189Thr|3567/5835|3567/5835|1189/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2269C>T|||||2269|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2269C>T|||||2269|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3769C>T|||||3769|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3769C>T|||||3769|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4687C>T|||||4687|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4687C>T|||||4687|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3567C>T|||||3567|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3567C>T|||||3567|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:15:1,14:1:39:14:545:-45.4997,-0.618886,0

-NC_045512.2	6367	.	G	A	0.00155336	.	AB=0.133333;ABP=38.0434;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=11.6962;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.93571;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=154;QR=995;RO=26;RPL=2;RPP=3.0103;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6102G>A|p.Gln2034Gln|6102/21291|6102/21291|2034/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6102G>A|p.Gln2034Gln|6102/13218|6102/13218|2034/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3648G>A|p.Gln1216Gln|3648/5835|3648/5835|1216/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3648G>A|p.Gln1216Gln|3648/5835|3648/5835|1216/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2188G>A|||||2188|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2188G>A|||||2188|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3688G>A|||||3688|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3688G>A|||||3688|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4606G>A|||||4606|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4606G>A|||||4606|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3648G>A|||||3648|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3648G>A|||||3648|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:30:26,4:26:995:4:154:-5.20269,0,-80.8329

-NC_045512.2	6376	.	T	G	2.59457E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=7.35324;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.8441;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=1063;RO=28;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6111T>G|p.Asp2037Glu|6111/21291|6111/21291|2037/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6111T>G|p.Asp2037Glu|6111/13218|6111/13218|2037/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3657T>G|p.Asp1219Glu|3657/5835|3657/5835|1219/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3657T>G|p.Asp1219Glu|3657/5835|3657/5835|1219/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2179T>G|||||2179|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2179T>G|||||2179|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3679T>G|||||3679|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3679T>G|||||3679|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4597T>G|||||4597|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4597T>G|||||4597|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3657T>G|||||3657|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3657T>G|||||3657|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:28,2:28:1063:2:78:0,-1.62743,-88.5654

-NC_045512.2	6405	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.8789;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1086;RO=29;RPL=1;RPP=5.18177;RPPR=3.08518;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=3.08518;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6140T>C|p.Val2047Ala|6140/21291|6140/21291|2047/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6140T>C|p.Val2047Ala|6140/13218|6140/13218|2047/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3686T>C|p.Val1229Ala|3686/5835|3686/5835|1229/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3686T>C|p.Val1229Ala|3686/5835|3686/5835|1229/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2150T>C|||||2150|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2150T>C|||||2150|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3650T>C|||||3650|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3650T>C|||||3650|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4568T>C|||||4568|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4568T>C|||||4568|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3686T>C|||||3686|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3686T>C|||||3686|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1086:1:13:0,-7.73091,-96.7432

-NC_045512.2	6471	.	C	A	2.17051E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.5056;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1044;RO=29;RPL=0;RPP=5.18177;RPPR=3.08518;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=3.08518;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6206C>A|p.Thr2069Asn|6206/21291|6206/21291|2069/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6206C>A|p.Thr2069Asn|6206/13218|6206/13218|2069/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3752C>A|p.Thr1251Asn|3752/5835|3752/5835|1251/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3752C>A|p.Thr1251Asn|3752/5835|3752/5835|1251/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2084C>A|||||2084|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2084C>A|||||2084|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3584C>A|||||3584|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3584C>A|||||3584|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4502C>A|||||4502|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4502C>A|||||4502|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3752C>A|||||3752|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3752C>A|||||3752|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1044:1:32:0,-5.83159,-91.0697

-NC_045512.2	6472	.	CGA	CA,AGA	2.02509E-14	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D1M,1X2M;DP=31;DPB=30.6667;DPRA=0,0;EPP=5.18177,5.18177;EPPR=65.983;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=36.7744;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=37,39;QR=1034;RO=29;RPL=0,1;RPP=5.18177,5.18177;RPPR=3.08518;RPR=1,0;RUN=1,1;SAF=1,0;SAP=5.18177,5.18177;SAR=0,1;SRF=15;SRP=3.08518;SRR=14;TYPE=del,snp;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6208delG|p.Glu2070fs|6208/21291|6208/21291|2070/7096||,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6208delG|p.Glu2070fs|6208/13218|6208/13218|2070/4405||,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3754delG|p.Glu1252fs|3754/5835|3754/5835|1252/1944||WARNING_TRANSCRIPT_NO_START_CODON,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3754delG|p.Glu1252fs|3754/5835|3754/5835|1252/1944||WARNING_TRANSCRIPT_NO_START_CODON,AGA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6207C>A|p.Thr2069Thr|6207/21291|6207/21291|2069/7096||,AGA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6207C>A|p.Thr2069Thr|6207/13218|6207/13218|2069/4405||,AGA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3753C>A|p.Thr1251Thr|3753/5835|3753/5835|1251/1944||WARNING_TRANSCRIPT_NO_START_CODON,AGA|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3753C>A|p.Thr1251Thr|3753/5835|3753/5835|1251/1944||WARNING_TRANSCRIPT_NO_START_CODON,AGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2083C>A|||||2083|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2082delG|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,AGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2083C>A|||||2083|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2082delG|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,AGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3583C>A|||||3583|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3582delG|||||3582|WARNING_TRANSCRIPT_NO_START_CODON,AGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3583C>A|||||3583|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3582delG|||||3582|WARNING_TRANSCRIPT_NO_START_CODON,AGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4501C>A|||||4501|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4500delG|||||4500|WARNING_TRANSCRIPT_NO_START_CODON,AGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4501C>A|||||4501|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4500delG|||||4500|WARNING_TRANSCRIPT_NO_START_CODON,AGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3753C>A|||||3753|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3754delG|||||3754|WARNING_TRANSCRIPT_NO_START_CODON,AGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3753C>A|||||3753|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3754delG|||||3754|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:29,1,1:29:1034:1,1:37,39:0,-5.71279,-89.662,-5.51405,-86.7561,-89.4825

-NC_045512.2	6500	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.3944;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1391;RO=36;RPL=0;RPP=5.18177;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=5.18177;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6235C>T|p.Pro2079Ser|6235/21291|6235/21291|2079/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6235C>T|p.Pro2079Ser|6235/13218|6235/13218|2079/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3781C>T|p.Pro1261Ser|3781/5835|3781/5835|1261/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3781C>T|p.Pro1261Ser|3781/5835|3781/5835|1261/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2055C>T|||||2055|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2055C>T|||||2055|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3555C>T|||||3555|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3555C>T|||||3555|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4473C>T|||||4473|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4473C>T|||||4473|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3781C>T|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3781C>T|||||3781|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1391:1:39:0,-7.24155,-121.576

-NC_045512.2	6648	.	C	G	1.06832E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=7.35324;EPPR=94.2121;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.4753;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=1601;RO=42;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6383C>G|p.Ala2128Gly|6383/21291|6383/21291|2128/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6383C>G|p.Ala2128Gly|6383/13218|6383/13218|2128/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3929C>G|p.Ala1310Gly|3929/5835|3929/5835|1310/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3929C>G|p.Ala1310Gly|3929/5835|3929/5835|1310/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1907C>G|||||1907|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1907C>G|||||1907|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3407C>G|||||3407|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3407C>G|||||3407|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4325C>G|||||4325|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4325C>G|||||4325|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3929C>G|||||3929|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3929C>G|||||3929|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:42,2:42:1601:2:78:0,-5.84185,-136.946

-NC_045512.2	6721	.	A	T	0.194957	.	AB=0.15625;ABP=35.8538;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=13.8677;EPPR=38.4777;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.081;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=193;QR=1010;RO=27;RPL=1;RPP=6.91895;RPPR=21.1059;RPR=4;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=9;SRP=9.52472;SRR=18;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6456A>T|p.Thr2152Thr|6456/21291|6456/21291|2152/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6456A>T|p.Thr2152Thr|6456/13218|6456/13218|2152/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4002A>T|p.Thr1334Thr|4002/5835|4002/5835|1334/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4002A>T|p.Thr1334Thr|4002/5835|4002/5835|1334/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1834A>T|||||1834|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1834A>T|||||1834|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3334A>T|||||3334|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3334A>T|||||3334|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4252A>T|||||4252|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4252A>T|||||4252|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4002A>T|||||4002|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4002A>T|||||4002|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:32:27,5:27:1010:5:193:-8.1084,0,-81.5714

-NC_045512.2	6761	.	A	T	3.18833E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.0953;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=970;RO=25;RPL=1;RPP=5.18177;RPPR=28.1125;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=28.1125;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6496A>T|p.Thr2166Ser|6496/21291|6496/21291|2166/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6496A>T|p.Thr2166Ser|6496/13218|6496/13218|2166/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4042A>T|p.Thr1348Ser|4042/5835|4042/5835|1348/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4042A>T|p.Thr1348Ser|4042/5835|4042/5835|1348/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1794A>T|||||1794|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1794A>T|||||1794|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3294A>T|||||3294|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3294A>T|||||3294|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4212A>T|||||4212|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4212A>T|||||4212|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4042A>T|||||4042|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4042A>T|||||4042|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:970:1:19:0,-5.92681,-85.7134

-NC_045512.2	6785	.	A	T	1.65294E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.7861;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=963;RO=25;RPL=0;RPP=5.18177;RPPR=34.3664;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=34.3664;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6520A>T|p.Thr2174Ser|6520/21291|6520/21291|2174/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6520A>T|p.Thr2174Ser|6520/13218|6520/13218|2174/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4066A>T|p.Thr1356Ser|4066/5835|4066/5835|1356/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4066A>T|p.Thr1356Ser|4066/5835|4066/5835|1356/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1770A>T|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1770A>T|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3270A>T|||||3270|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3270A>T|||||3270|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4188A>T|||||4188|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4188A>T|||||4188|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4066A>T|||||4066|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4066A>T|||||4066|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:963:1:16:0,-6.2268,-85.3846

-NC_045512.2	6859	.	AGC	AC	2.57295E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=25;DPB=24.6667;DPRA=0;EPP=5.18177;EPPR=26.1727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.5266;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=885;RO=24;RPL=1;RPP=5.18177;RPPR=55.1256;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=26.1727;SRR=20;TYPE=del;ANN=AC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6595delG|p.Ala2199fs|6595/21291|6595/21291|2199/7096||,AC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6595delG|p.Ala2199fs|6595/13218|6595/13218|2199/4405||,AC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4141delG|p.Ala1381fs|4141/5835|4141/5835|1381/1944||WARNING_TRANSCRIPT_NO_START_CODON,AC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4141delG|p.Ala1381fs|4141/5835|4141/5835|1381/1944||WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1695delG|||||1695|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1695delG|||||1695|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3195delG|||||3195|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3195delG|||||3195|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4113delG|||||4113|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4113delG|||||4113|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4983delG|||||4983|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4983delG|||||4983|WARNING_TRANSCRIPT_NO_START_CODON,AC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4141delG|||||4141|WARNING_TRANSCRIPT_NO_START_CODON,AC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4141delG|||||4141|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:885:1:33:0,-4.22661,-76.6678

-NC_045512.2	6915	.	A	T	2.63807E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.0114;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=263;RO=7;RPL=1;RPP=5.18177;RPPR=3.32051;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6650A>T|p.Tyr2217Phe|6650/21291|6650/21291|2217/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6650A>T|p.Tyr2217Phe|6650/13218|6650/13218|2217/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4196A>T|p.Tyr1399Phe|4196/5835|4196/5835|1399/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4196A>T|p.Tyr1399Phe|4196/5835|4196/5835|1399/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1640A>T|||||1640|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1640A>T|||||1640|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3140A>T|||||3140|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3140A>T|||||3140|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4058A>T|||||4058|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4058A>T|||||4058|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4928A>T|||||4928|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4928A>T|||||4928|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4196A>T|||||4196|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4196A>T|||||4196|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:8:7,1:7:263:1:16:0,-0.808257,-22.4266

-NC_045512.2	6921	.	A	C	2.63807E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.0114;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=250;RO=7;RPL=1;RPP=5.18177;RPPR=3.32051;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6656A>C|p.Lys2219Thr|6656/21291|6656/21291|2219/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6656A>C|p.Lys2219Thr|6656/13218|6656/13218|2219/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4202A>C|p.Lys1401Thr|4202/5835|4202/5835|1401/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4202A>C|p.Lys1401Thr|4202/5835|4202/5835|1401/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1634A>C|||||1634|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1634A>C|||||1634|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3134A>C|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3134A>C|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4052A>C|||||4052|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4052A>C|||||4052|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4922A>C|||||4922|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4922A>C|||||4922|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4202A>C|||||4202|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4202A>C|||||4202|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:8:7,1:7:250:1:16:0,-0.808257,-21.2383

-NC_045512.2	6924	.	CACCT	AACCG	3.3211E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7812;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=259;RO=7;RPL=0;RPP=5.18177;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=complex;ANN=AACCG|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6659_6663delCACCTinsAACCG|p.Ser2220*|6659/21291|6659/21291|2220/7096||,AACCG|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6659_6663delCACCTinsAACCG|p.Ser2220*|6659/13218|6659/13218|2220/4405||,AACCG|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4205_4209delCACCTinsAACCG|p.Ser1402*|4205/5835|4205/5835|1402/1944||WARNING_TRANSCRIPT_NO_START_CODON,AACCG|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4205_4209delCACCTinsAACCG|p.Ser1402*|4205/5835|4205/5835|1402/1944||WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1631_-1627delCACCTinsAACCG|||||1631|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1631_-1627delCACCTinsAACCG|||||1631|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3131_-3127delCACCTinsAACCG|||||3131|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3131_-3127delCACCTinsAACCG|||||3131|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4049_-4045delCACCTinsAACCG|||||4049|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4049_-4045delCACCTinsAACCG|||||4049|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4919_-4915delCACCTinsAACCG|||||4919|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4919_-4915delCACCTinsAACCG|||||4919|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4205_*4209delCACCTinsAACCG|||||4205|WARNING_TRANSCRIPT_NO_START_CODON,AACCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4205_*4209delCACCTinsAACCG|||||4205|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:8:7,1:7:259:1:17:0,-0.708261,-21.9623

-NC_045512.2	6940	.	A	C	2.09551E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.2417;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=263;RO=7;RPL=1;RPP=5.18177;RPPR=3.32051;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.32051;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6675A>C|p.Lys2225Asn|6675/21291|6675/21291|2225/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6675A>C|p.Lys2225Asn|6675/13218|6675/13218|2225/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4221A>C|p.Lys1407Asn|4221/5835|4221/5835|1407/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4221A>C|p.Lys1407Asn|4221/5835|4221/5835|1407/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1615A>C|||||1615|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1615A>C|||||1615|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3115A>C|||||3115|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3115A>C|||||3115|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4033A>C|||||4033|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4033A>C|||||4033|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4903A>C|||||4903|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4903A>C|||||4903|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4221A>C|||||4221|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4221A>C|||||4221|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:8:7,1:7:263:1:15:0,-0.908253,-22.5266

-NC_045512.2	7008	.	C	A	0.00337556	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.1594;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=117;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6743C>A|p.Ala2248Asp|6743/21291|6743/21291|2248/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6743C>A|p.Ala2248Asp|6743/13218|6743/13218|2248/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4289C>A|p.Ala1430Asp|4289/5835|4289/5835|1430/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4289C>A|p.Ala1430Asp|4289/5835|4289/5835|1430/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1547C>A|||||1547|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1547C>A|||||1547|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3047C>A|||||3047|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3047C>A|||||3047|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3965C>A|||||3965|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3965C>A|||||3965|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4835C>A|||||4835|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4835C>A|||||4835|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4289C>A|||||4289|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4289C>A|||||4289|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:117:1:16:-0.395863,0,-9.70626

-NC_045512.2	7015	.	A	G	0.00213017	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.6199;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=117;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6750A>G|p.Leu2250Leu|6750/21291|6750/21291|2250/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6750A>G|p.Leu2250Leu|6750/13218|6750/13218|2250/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4296A>G|p.Leu1432Leu|4296/5835|4296/5835|1432/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4296A>G|p.Leu1432Leu|4296/5835|4296/5835|1432/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1540A>G|||||1540|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1540A>G|||||1540|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3040A>G|||||3040|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3040A>G|||||3040|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3958A>G|||||3958|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3958A>G|||||3958|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4828A>G|||||4828|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4828A>G|||||4828|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4296A>G|||||4296|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4296A>G|||||4296|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:117:1:14:-0.19587,0,-9.70626

-NC_045512.2	7050	.	A	T	0.00337552	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.1594;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=119;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6785A>T|p.Tyr2262Phe|6785/21291|6785/21291|2262/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6785A>T|p.Tyr2262Phe|6785/13218|6785/13218|2262/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4331A>T|p.Tyr1444Phe|4331/5835|4331/5835|1444/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4331A>T|p.Tyr1444Phe|4331/5835|4331/5835|1444/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1505A>T|||||1505|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1505A>T|||||1505|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3005A>T|||||3005|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3005A>T|||||3005|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3923A>T|||||3923|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3923A>T|||||3923|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4793A>T|||||4793|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4793A>T|||||4793|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4331A>T|||||4331|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4331A>T|||||4331|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:119:1:16:-0.395863,0,-9.89127

-NC_045512.2	7067	.	G	T	0.00337556	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.1594;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=117;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6802G>T|p.Glu2268*|6802/21291|6802/21291|2268/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6802G>T|p.Glu2268*|6802/13218|6802/13218|2268/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4348G>T|p.Glu1450*|4348/5835|4348/5835|1450/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4348G>T|p.Glu1450*|4348/5835|4348/5835|1450/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1488G>T|||||1488|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1488G>T|||||1488|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2988G>T|||||2988|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2988G>T|||||2988|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3906G>T|||||3906|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3906G>T|||||3906|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4776G>T|||||4776|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4776G>T|||||4776|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4348G>T|||||4348|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4348G>T|||||4348|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:117:1:16:-0.395863,0,-9.70626

-NC_045512.2	7085	.	A	T	0.00534857	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.6989;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=117;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6820A>T|p.Thr2274Ser|6820/21291|6820/21291|2274/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6820A>T|p.Thr2274Ser|6820/13218|6820/13218|2274/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4366A>T|p.Thr1456Ser|4366/5835|4366/5835|1456/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4366A>T|p.Thr1456Ser|4366/5835|4366/5835|1456/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1470A>T|||||1470|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1470A>T|||||1470|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2970A>T|||||2970|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2970A>T|||||2970|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3888A>T|||||3888|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3888A>T|||||3888|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4758A>T|||||4758|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4758A>T|||||4758|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4366A>T|||||4366|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4366A>T|||||4366|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:117:1:18:-0.595853,0,-9.70626

-NC_045512.2	7103	.	A	T	0.00337568	.	AB=0.25;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.1594;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=114;RO=3;RPL=1;RPP=5.18177;RPPR=9.52472;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6838A>T|p.Thr2280Ser|6838/21291|6838/21291|2280/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6838A>T|p.Thr2280Ser|6838/13218|6838/13218|2280/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4384A>T|p.Thr1462Ser|4384/5835|4384/5835|1462/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4384A>T|p.Thr1462Ser|4384/5835|4384/5835|1462/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1452A>T|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1452A>T|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2952A>T|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2952A>T|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3870A>T|||||3870|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3870A>T|||||3870|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4740A>T|||||4740|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4740A>T|||||4740|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4989A>T|||||4989|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4989A>T|||||4989|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4384A>T|||||4384|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4384A>T|||||4384|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4:3,1:3:114:1:16:-0.395863,0,-9.42823

-NC_045512.2	7117	.	T	G	0.0107164	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.06079;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=67;RO=2;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6852T>G|p.Gly2284Gly|6852/21291|6852/21291|2284/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6852T>G|p.Gly2284Gly|6852/13218|6852/13218|2284/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4398T>G|p.Gly1466Gly|4398/5835|4398/5835|1466/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4398T>G|p.Gly1466Gly|4398/5835|4398/5835|1466/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1438T>G|||||1438|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1438T>G|||||1438|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2938T>G|||||2938|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2938T>G|||||2938|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3856T>G|||||3856|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3856T>G|||||3856|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4726T>G|||||4726|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4726T>G|||||4726|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4975T>G|||||4975|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4975T>G|||||4975|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4398T>G|||||4398|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4398T>G|||||4398|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:67:1:16:-0.696893,0,-5.46005

-NC_045512.2	7307	.	C	G	0.00131939	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.09899;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=235;RO=7;RPL=0;RPP=5.18177;RPPR=18.2106;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=18.2106;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7042C>G|p.Gln2348Glu|7042/21291|7042/21291|2348/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7042C>G|p.Gln2348Glu|7042/13218|7042/13218|2348/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4588C>G|p.Gln1530Glu|4588/5835|4588/5835|1530/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4588C>G|p.Gln1530Glu|4588/5835|4588/5835|1530/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1248C>G|||||1248|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1248C>G|||||1248|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2748C>G|||||2748|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2748C>G|||||2748|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3666C>G|||||3666|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3666C>G|||||3666|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4536C>G|||||4536|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4536C>G|||||4536|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4785C>G|||||4785|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4785C>G|||||4785|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4588C>G|||||4588|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4588C>G|||||4588|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:235:1:33:-0.890895,0,-19.071

-NC_045512.2	7685	.	T	A	1.29273E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.2377;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=740;RO=20;RPL=1;RPP=5.18177;RPPR=24.2907;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=24.2907;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7420T>A|p.Ser2474Thr|7420/21291|7420/21291|2474/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7420T>A|p.Ser2474Thr|7420/13218|7420/13218|2474/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4966T>A|p.Ser1656Thr|4966/5835|4966/5835|1656/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4966T>A|p.Ser1656Thr|4966/5835|4966/5835|1656/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-870T>A|||||870|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-870T>A|||||870|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2370T>A|||||2370|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2370T>A|||||2370|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3288T>A|||||3288|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3288T>A|||||3288|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4158T>A|||||4158|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4158T>A|||||4158|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4407T>A|||||4407|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4407T>A|||||4407|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4966T>A|||||4966|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4966T>A|||||4966|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:740:1:37:0,-2.6238,-63.2302

-NC_045512.2	7693	.	G	T	6.01924E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.0943;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=483;RO=14;RPL=1;RPP=5.18177;RPPR=12.937;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=12.937;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7428G>T|p.Gln2476His|7428/21291|7428/21291|2476/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7428G>T|p.Gln2476His|7428/13218|7428/13218|2476/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4974G>T|p.Gln1658His|4974/5835|4974/5835|1658/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4974G>T|p.Gln1658His|4974/5835|4974/5835|1658/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-862G>T|||||862|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-862G>T|||||862|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2362G>T|||||2362|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2362G>T|||||2362|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3280G>T|||||3280|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3280G>T|||||3280|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4150G>T|||||4150|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4150G>T|||||4150|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4399G>T|||||4399|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4399G>T|||||4399|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4993G>T|||||4993|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4993G>T|||||4993|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4974G>T|||||4974|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4974G>T|||||4974|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:483:1:29:0,-1.61579,-40.8965

-NC_045512.2	7871	.	T	G	14.9387	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.40716;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=156;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.0103;SRR=2;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7606T>G|p.Leu2536Val|7606/21291|7606/21291|2536/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7606T>G|p.Leu2536Val|7606/13218|7606/13218|2536/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5152T>G|p.Leu1718Val|5152/5835|5152/5835|1718/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5152T>G|p.Leu1718Val|5152/5835|5152/5835|1718/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-684T>G|||||684|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-684T>G|||||684|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2184T>G|||||2184|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2184T>G|||||2184|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3102T>G|||||3102|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3102T>G|||||3102|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3972T>G|||||3972|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3972T>G|||||3972|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4221T>G|||||4221|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4221T>G|||||4221|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4815T>G|||||4815|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4815T>G|||||4815|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:156:2:75:-5.31392,0,-12.6111

-NC_045512.2	8208	.	C	T	1.59375E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=14.7363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1206;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=583;RO=15;RPL=0;RPP=5.18177;RPPR=14.7363;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=35.5824;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7943C>T|p.Thr2648Ile|7943/21291|7943/21291|2648/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7943C>T|p.Thr2648Ile|7943/13218|7943/13218|2648/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5489C>T|p.Thr1830Ile|5489/5835|5489/5835|1830/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5489C>T|p.Thr1830Ile|5489/5835|5489/5835|1830/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-347C>T|||||347|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-347C>T|||||347|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1847C>T|||||1847|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1847C>T|||||1847|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2765C>T|||||2765|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2765C>T|||||2765|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3635C>T|||||3635|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3635C>T|||||3635|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3884C>T|||||3884|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3884C>T|||||3884|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4478C>T|||||4478|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4478C>T|||||4478|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4817C>T|||||4817|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4817C>T|||||4817|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:583:1:39:0,-0.919915,-48.9167

-NC_045512.2	8271	.	G	T	1.96799E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.7266;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=965;RO=25;RPL=0;RPP=5.18177;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=5.18177;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8006G>T|p.Ser2669Ile|8006/21291|8006/21291|2669/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8006G>T|p.Ser2669Ile|8006/13218|8006/13218|2669/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5552G>T|p.Ser1851Ile|5552/5835|5552/5835|1851/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5552G>T|p.Ser1851Ile|5552/5835|5552/5835|1851/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-284G>T|||||284|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-284G>T|||||284|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1784G>T|||||1784|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1784G>T|||||1784|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2702G>T|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2702G>T|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3572G>T|||||3572|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3572G>T|||||3572|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3821G>T|||||3821|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3821G>T|||||3821|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4415G>T|||||4415|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4415G>T|||||4415|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4754G>T|||||4754|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4754G>T|||||4754|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:965:1:38:0,-4.02951,-83.3675

-NC_045512.2	8329	.	TGGTGC	TGTGC	2.31588E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D4M;DP=24;DPB=23.8333;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.2631;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=838;RO=23;RPL=0;RPP=5.18177;RPPR=3.86001;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.86001;SRR=13;TYPE=del;ANN=TGTGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8066delG|p.Gly2689fs|8066/21291|8066/21291|2689/7096||,TGTGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8066delG|p.Gly2689fs|8066/13218|8066/13218|2689/4405||,TGTGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5612delG|p.Gly1871fs|5612/5835|5612/5835|1871/1944||WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5612delG|p.Gly1871fs|5612/5835|5612/5835|1871/1944||WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-224delG|||||224|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-224delG|||||224|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1724delG|||||1724|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1724delG|||||1724|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2642delG|||||2642|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2642delG|||||2642|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3512delG|||||3512|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3512delG|||||3512|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3761delG|||||3761|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3761delG|||||3761|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4355delG|||||4355|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4355delG|||||4355|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4694delG|||||4694|WARNING_TRANSCRIPT_NO_START_CODON,TGTGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4694delG|||||4694|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:838:1:37:0,-3.52689,-72.0445

-NC_045512.2	8481	.	CTTTTAAG	CTTTTTAAG	5.84477E-7	.	AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M1I7M;DP=22;DPB=22.25;DPRA=0;EPP=7.35324;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.8211;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=759;RO=20;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=ins;ANN=CTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8220dupT|p.Lys2741fs|8221/21291|8221/21291|2741/7096||,CTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8220dupT|p.Lys2741fs|8221/13218|8221/13218|2741/4405||,CTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5766dupT|p.Lys1923fs|5767/5835|5767/5835|1923/1944||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5766dupT|p.Lys1923fs|5767/5835|5767/5835|1923/1944||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-70dupT|||||69|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-70dupT|||||69|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1570dupT|||||1569|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1570dupT|||||1569|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2488dupT|||||2487|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2488dupT|||||2487|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3358dupT|||||3357|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3358dupT|||||3357|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3607dupT|||||3606|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3607dupT|||||3606|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4201dupT|||||4200|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4201dupT|||||4200|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4540dupT|||||4539|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4540dupT|||||4539|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4957dupT|||||4956|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4957dupT|||||4956|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:22:20,2:20:759:2:76:-0.592151,0,-62.0175

-NC_045512.2	8604	.	T	A	8.92671E-5	.	AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.7924;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=390;RO=10;RPL=1;RPP=5.18177;RPPR=24.725;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=24.725;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8339T>A|p.Phe2780Tyr|8339/21291|8339/21291|2780/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8339T>A|p.Phe2780Tyr|8339/13218|8339/13218|2780/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.50T>A|p.Phe17Tyr|50/1500|50/1500|17/499||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.50T>A|p.Phe17Tyr|50/1500|50/1500|17/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1451T>A|||||1451|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1451T>A|||||1451|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2369T>A|||||2369|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2369T>A|||||2369|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3239T>A|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3239T>A|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3488T>A|||||3488|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3488T>A|||||3488|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4082T>A|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4082T>A|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4421T>A|||||4421|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4421T>A|||||4421|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4838T>A|||||4838|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4838T>A|||||4838|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*50T>A|||||50|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*50T>A|||||50|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:10,1:10:390:1:38:-0.485939,0,-32.1474

-NC_045512.2	8660	.	C	A	0.00104849	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.32884;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=232;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8395C>A|p.His2799Asn|8395/21291|8395/21291|2799/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8395C>A|p.His2799Asn|8395/13218|8395/13218|2799/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.106C>A|p.His36Asn|106/1500|106/1500|36/499||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.106C>A|p.His36Asn|106/1500|106/1500|36/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1395C>A|||||1395|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1395C>A|||||1395|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2313C>A|||||2313|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2313C>A|||||2313|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3183C>A|||||3183|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3183C>A|||||3183|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3432C>A|||||3432|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3432C>A|||||3432|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4026C>A|||||4026|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4026C>A|||||4026|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4365C>A|||||4365|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4365C>A|||||4365|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4782C>A|||||4782|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4782C>A|||||4782|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*106C>A|||||106|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*106C>A|||||106|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:232:1:32:-0.791073,0,-18.7973

-NC_045512.2	8941	.	TGGTA	TGTA	1.77522E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=14;DPB=13.8;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=494;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=31.2394;SRR=0;TYPE=del;ANN=TGTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8678delG|p.Gly2893fs|8678/21291|8678/21291|2893/7096||,TGTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8678delG|p.Gly2893fs|8678/13218|8678/13218|2893/4405||,TGTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.389delG|p.Gly130fs|389/1500|389/1500|130/499||WARNING_TRANSCRIPT_NO_START_CODON,TGTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.389delG|p.Gly130fs|389/1500|389/1500|130/499||WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1112delG|||||1112|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1112delG|||||1112|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2030delG|||||2030|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2030delG|||||2030|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2900delG|||||2900|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2900delG|||||2900|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3149delG|||||3149|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3149delG|||||3149|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3743delG|||||3743|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3743delG|||||3743|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4082delG|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4082delG|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4499delG|||||4499|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4499delG|||||4499|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*389delG|||||389|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*389delG|||||389|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:494:1:38:0,-0.417151,-41.0105

-NC_045512.2	9257	.	G	A	1.41193E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.9391;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=489;RO=13;RPL=1;RPP=5.18177;RPPR=31.2394;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=31.2394;SRR=13;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8992G>A|p.Val2998Ile|8992/21291|8992/21291|2998/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8992G>A|p.Val2998Ile|8992/13218|8992/13218|2998/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.703G>A|p.Val235Ile|703/1500|703/1500|235/499||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.703G>A|p.Val235Ile|703/1500|703/1500|235/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-798G>A|||||798|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-798G>A|||||798|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1716G>A|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1716G>A|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2586G>A|||||2586|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2586G>A|||||2586|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2835G>A|||||2835|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2835G>A|||||2835|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3429G>A|||||3429|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3429G>A|||||3429|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3768G>A|||||3768|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3768G>A|||||3768|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4185G>A|||||4185|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4185G>A|||||4185|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*703G>A|||||703|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*703G>A|||||703|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:489:1:37:0,-0.516591,-40.6586

-NC_045512.2	9799	.	T	C	0.00330346	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.18096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=262;RO=7;RPL=0;RPP=5.18177;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=10.7656;SRR=1;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9534T>C|p.Ala3178Ala|9534/21291|9534/21291|3178/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9534T>C|p.Ala3178Ala|9534/13218|9534/13218|3178/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1245T>C|p.Ala415Ala|1245/1500|1245/1500|415/499||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1245T>C|p.Ala415Ala|1245/1500|1245/1500|415/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-256T>C|||||256|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-256T>C|||||256|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1174T>C|||||1174|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1174T>C|||||1174|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2044T>C|||||2044|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2044T>C|||||2044|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2293T>C|||||2293|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2293T>C|||||2293|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2887T>C|||||2887|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2887T>C|||||2887|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3226T>C|||||3226|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3226T>C|||||3226|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3643T>C|||||3643|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3643T>C|||||3643|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1245T>C|||||1245|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1245T>C|||||1245|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:262:1:37:-1.28959,0,-21.5305

-NC_045512.2	9844	.	G	A	0.00330346	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.18096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=272;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=18.2106;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9579G>A|p.Leu3193Leu|9579/21291|9579/21291|3193/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9579G>A|p.Leu3193Leu|9579/13218|9579/13218|3193/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1290G>A|p.Leu430Leu|1290/1500|1290/1500|430/499||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1290G>A|p.Leu430Leu|1290/1500|1290/1500|430/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-211G>A|||||211|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-211G>A|||||211|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1129G>A|||||1129|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1129G>A|||||1129|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1999G>A|||||1999|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1999G>A|||||1999|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2248G>A|||||2248|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2248G>A|||||2248|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2842G>A|||||2842|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2842G>A|||||2842|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3181G>A|||||3181|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3181G>A|||||3181|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3598G>A|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3598G>A|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1290G>A|||||1290|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1290G>A|||||1290|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:272:1:37:-1.28959,0,-22.439

-NC_045512.2	10078	.	C	T	5.1623E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.1557;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=697;RO=20;RPL=0;RPP=5.18177;RPPR=9.95901;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=9.95901;SRR=6;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9813C>T|p.Phe3271Phe|9813/21291|9813/21291|3271/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9813C>T|p.Phe3271Phe|9813/13218|9813/13218|3271/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.24C>T|p.Phe8Phe|24/918|24/918|8/305||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.24C>T|p.Phe8Phe|24/918|24/918|8/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-895C>T|||||895|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-895C>T|||||895|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1765C>T|||||1765|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1765C>T|||||1765|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2014C>T|||||2014|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2014C>T|||||2014|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2608C>T|||||2608|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2608C>T|||||2608|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2947C>T|||||2947|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2947C>T|||||2947|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3364C>T|||||3364|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3364C>T|||||3364|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1524C>T|||||1524|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1524C>T|||||1524|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*24C>T|||||24|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*24C>T|||||24|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:697:1:33:0,-3.02249,-59.75

-NC_045512.2	10204	.	T	A	2.90158E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=7.35324;EPPR=11.3621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.4292;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1009;RO=26;RPL=1;RPP=3.0103;RPPR=4.34659;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=23;SRP=36.4176;SRR=3;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9939T>A|p.Leu3313Leu|9939/21291|9939/21291|3313/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9939T>A|p.Leu3313Leu|9939/13218|9939/13218|3313/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.150T>A|p.Leu50Leu|150/918|150/918|50/305||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.150T>A|p.Leu50Leu|150/918|150/918|50/305||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-769T>A|||||769|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-769T>A|||||769|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1639T>A|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1639T>A|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1888T>A|||||1888|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1888T>A|||||1888|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2482T>A|||||2482|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2482T>A|||||2482|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2821T>A|||||2821|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2821T>A|||||2821|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3238T>A|||||3238|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3238T>A|||||3238|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1650T>A|||||1650|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1650T>A|||||1650|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*150T>A|||||150|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*150T>A|||||150|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:26,2:26:1009:2:77:0,-1.1197,-83.8113

-NC_045512.2	10228	.	C	T	0.0579076	.	AB=0.145833;ABP=55.3066;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=18.2106;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.31079;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=1591;RO=41;RPL=3;RPP=3.32051;RPPR=3.06326;RPR=4;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=21;SRP=3.06326;SRR=20;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9963C>T|p.Leu3321Leu|9963/21291|9963/21291|3321/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9963C>T|p.Leu3321Leu|9963/13218|9963/13218|3321/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.174C>T|p.Leu58Leu|174/918|174/918|58/305||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.174C>T|p.Leu58Leu|174/918|174/918|58/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-745C>T|||||745|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-745C>T|||||745|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1615C>T|||||1615|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1615C>T|||||1615|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1864C>T|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1864C>T|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2458C>T|||||2458|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2458C>T|||||2458|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2797C>T|||||2797|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2797C>T|||||2797|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3214C>T|||||3214|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3214C>T|||||3214|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1674C>T|||||1674|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1674C>T|||||1674|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*174C>T|||||174|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*174C>T|||||174|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:48:41,7:41:1591:7:267:-9.94373,0,-129.006

-NC_045512.2	10284	.	T	G	3.61623E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=96.5684;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=66.5925;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1763;RO=47;RPL=1;RPP=5.18177;RPPR=3.0565;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=3.0565;SRR=24;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10019T>G|p.Val3340Gly|10019/21291|10019/21291|3340/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10019T>G|p.Val3340Gly|10019/13218|10019/13218|3340/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.230T>G|p.Val77Gly|230/918|230/918|77/305||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.230T>G|p.Val77Gly|230/918|230/918|77/305||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-689T>G|||||689|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-689T>G|||||689|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1559T>G|||||1559|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1559T>G|||||1559|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1808T>G|||||1808|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1808T>G|||||1808|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2402T>G|||||2402|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2402T>G|||||2402|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2741T>G|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2741T>G|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3158T>G|||||3158|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3158T>G|||||3158|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1730T>G|||||1730|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1730T>G|||||1730|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*230T>G|||||230|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*230T>G|||||230|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:47,1:47:1763:1:12:0,-13.2494,-157.719

-NC_045512.2	10300	.	G	T	1.95969E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=11.6962;EPPR=90.0666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.9289;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=154;QR=1705;RO=44;RPL=2;RPP=3.0103;RPPR=3.20771;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=22;SRP=3.0103;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10035G>T|p.Met3345Ile|10035/21291|10035/21291|3345/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10035G>T|p.Met3345Ile|10035/13218|10035/13218|3345/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.246G>T|p.Met82Ile|246/918|246/918|82/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.246G>T|p.Met82Ile|246/918|246/918|82/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-673G>T|||||673|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-673G>T|||||673|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1543G>T|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1543G>T|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1792G>T|||||1792|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1792G>T|||||1792|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2386G>T|||||2386|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2386G>T|||||2386|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2725G>T|||||2725|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2725G>T|||||2725|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3142G>T|||||3142|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3142G>T|||||3142|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1746G>T|||||1746|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1746G>T|||||1746|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*246G>T|||||246|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*246G>T|||||246|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:44,4:44:1705:4:154:0,-0.215848,-139.473

-NC_045512.2	10340	.	C	T	1.00842E-5	.	AB=0.111111;ABP=38.4777;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=3.73412;EPPR=39.2015;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.9731;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=117;QR=935;RO=24;RPL=3;RPP=9.52472;RPPR=55.1256;RPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=2;SRP=39.2015;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10075C>T|p.Pro3359Ser|10075/21291|10075/21291|3359/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10075C>T|p.Pro3359Ser|10075/13218|10075/13218|3359/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.286C>T|p.Pro96Ser|286/918|286/918|96/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.286C>T|p.Pro96Ser|286/918|286/918|96/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-633C>T|||||633|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-633C>T|||||633|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1503C>T|||||1503|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1503C>T|||||1503|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1752C>T|||||1752|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1752C>T|||||1752|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2346C>T|||||2346|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2346C>T|||||2346|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2685C>T|||||2685|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2685C>T|||||2685|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3102C>T|||||3102|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3102C>T|||||3102|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1786C>T|||||1786|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1786C>T|||||1786|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*286C>T|||||286|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*286C>T|||||286|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:27:24,3:24:935:3:117:-2.78257,0,-76.3379

-NC_045512.2	10386	.	CTTTTTCA	CTTTTCA	1.31392E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D6M;DP=40;DPB=39.875;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.704;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1484;RO=39;RPL=1;RPP=5.18177;RPPR=4.40227;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=4.40227;SRR=22;TYPE=del;ANN=CTTTTCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10126delT|p.Ser3376fs|10126/21291|10126/21291|3376/7096||,CTTTTCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10126delT|p.Ser3376fs|10126/13218|10126/13218|3376/4405||,CTTTTCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.337delT|p.Ser113fs|337/918|337/918|113/305||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.337delT|p.Ser113fs|337/918|337/918|113/305||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-582delT|||||582|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-582delT|||||582|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1452delT|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1452delT|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1701delT|||||1701|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1701delT|||||1701|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2295delT|||||2295|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2295delT|||||2295|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2634delT|||||2634|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2634delT|||||2634|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3051delT|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3051delT|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1837delT|||||1837|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1837delT|||||1837|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*337delT|||||337|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*337delT|||||337|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1484:1:38:0,-8.24393,-130.044

-NC_045512.2	10429	.	T	A	8.33286E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.4753;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1487;RO=39;RPL=0;RPP=5.18177;RPPR=5.73856;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=5.73856;SRR=23;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10164T>A|p.Val3388Val|10164/21291|10164/21291|3388/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10164T>A|p.Val3388Val|10164/13218|10164/13218|3388/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.375T>A|p.Val125Val|375/918|375/918|125/305||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.375T>A|p.Val125Val|375/918|375/918|125/305||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-544T>A|||||544|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-544T>A|||||544|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1414T>A|||||1414|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1414T>A|||||1414|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1663T>A|||||1663|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1663T>A|||||1663|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2257T>A|||||2257|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2257T>A|||||2257|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2596T>A|||||2596|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2596T>A|||||2596|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3013T>A|||||3013|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3013T>A|||||3013|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1875T>A|||||1875|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1875T>A|||||1875|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*375T>A|||||375|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*375T>A|||||375|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1487:1:39:0,-8.14463,-130.212

-NC_045512.2	10444	.	GAG	GG	1.31392E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=40;DPB=39.6667;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.704;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1452;RO=39;RPL=1;RPP=5.18177;RPPR=4.40227;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=4.40227;SRR=22;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10180delA|p.Arg3394fs|10180/21291|10180/21291|3394/7096||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10180delA|p.Arg3394fs|10180/13218|10180/13218|3394/4405||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.391delA|p.Arg131fs|391/918|391/918|131/305||WARNING_TRANSCRIPT_NO_START_CODON,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.391delA|p.Arg131fs|391/918|391/918|131/305||WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-528delA|||||528|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-528delA|||||528|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1398delA|||||1398|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1398delA|||||1398|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1647delA|||||1647|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1647delA|||||1647|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2241delA|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2241delA|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2580delA|||||2580|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2580delA|||||2580|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2997delA|||||2997|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2997delA|||||2997|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1891delA|||||1891|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1891delA|||||1891|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*391delA|||||391|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*391delA|||||391|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1452:1:38:0,-8.24393,-127.168

-NC_045512.2	10581	.	A	G	2.54949E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=7.35324;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.551;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=1235;RO=33;RPL=1;RPP=3.0103;RPPR=3.0761;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10316A>G|p.Asp3439Gly|10316/21291|10316/21291|3439/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10316A>G|p.Asp3439Gly|10316/13218|10316/13218|3439/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.527A>G|p.Asp176Gly|527/918|527/918|176/305||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.527A>G|p.Asp176Gly|527/918|527/918|176/305||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-392A>G|||||392|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-392A>G|||||392|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1262A>G|||||1262|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1262A>G|||||1262|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1511A>G|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1511A>G|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2105A>G|||||2105|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2105A>G|||||2105|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2444A>G|||||2444|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2444A>G|||||2444|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2861A>G|||||2861|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2861A>G|||||2861|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2027A>G|||||2027|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2027A>G|||||2027|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*527A>G|||||527|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*527A>G|||||527|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:33,2:33:1235:2:73:0,-3.60535,-104.505

-NC_045512.2	10746	.	A	T	5.66146E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.0634;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=613;RO=17;RPL=1;RPP=5.18177;RPPR=39.9253;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=39.9253;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10481A>T|p.Asn3494Ile|10481/21291|10481/21291|3494/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10481A>T|p.Asn3494Ile|10481/13218|10481/13218|3494/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.692A>T|p.Asn231Ile|692/918|692/918|231/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.692A>T|p.Asn231Ile|692/918|692/918|231/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-227A>T|||||227|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-227A>T|||||227|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1097A>T|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1097A>T|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1346A>T|||||1346|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1346A>T|||||1346|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1940A>T|||||1940|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1940A>T|||||1940|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2279A>T|||||2279|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2279A>T|||||2279|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2696A>T|||||2696|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2696A>T|||||2696|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2192A>T|||||2192|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2192A>T|||||2192|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*692A>T|||||692|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*692A>T|||||692|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:613:1:16:0,-3.81856,-53.8954

-NC_045512.2	10751	.	GTG	GG	2.67888E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=17;DPB=16.6667;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.9038;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=578;RO=16;RPL=1;RPP=5.18177;RPPR=37.7539;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=37.7539;SRR=16;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10487delT|p.Val3496fs|10487/21291|10487/21291|3496/7096||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10487delT|p.Val3496fs|10487/13218|10487/13218|3496/4405||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.698delT|p.Val233fs|698/918|698/918|233/305||WARNING_TRANSCRIPT_NO_START_CODON,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.698delT|p.Val233fs|698/918|698/918|233/305||WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-221delT|||||221|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-221delT|||||221|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1091delT|||||1091|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1091delT|||||1091|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1340delT|||||1340|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1340delT|||||1340|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1934delT|||||1934|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1934delT|||||1934|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2273delT|||||2273|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2273delT|||||2273|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2690delT|||||2690|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2690delT|||||2690|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2198delT|||||2198|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2198delT|||||2198|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*698delT|||||698|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*698delT|||||698|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:578:1:37:0,-1.41968,-48.6562

-NC_045512.2	10762	.	G	T	0.00208848	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.63963;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=215;RO=7;RPL=1;RPP=5.18177;RPPR=18.2106;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10497G>T|p.Lys3499Asn|10497/21291|10497/21291|3499/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10497G>T|p.Lys3499Asn|10497/13218|10497/13218|3499/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.708G>T|p.Lys236Asn|708/918|708/918|236/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.708G>T|p.Lys236Asn|708/918|708/918|236/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-211G>T|||||211|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-211G>T|||||211|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1081G>T|||||1081|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1081G>T|||||1081|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1330G>T|||||1330|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1330G>T|||||1330|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1924G>T|||||1924|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1924G>T|||||1924|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2263G>T|||||2263|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2263G>T|||||2263|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2680G>T|||||2680|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2680G>T|||||2680|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2208G>T|||||2208|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2208G>T|||||2208|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*708G>T|||||708|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*708G>T|||||708|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:215:1:35:-1.09039,0,-17.2439

-NC_045512.2	11074	.	CTTTTTTTTGTATGA	CTTTTTTTGTATGA	1.59375E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D13M;DP=16;DPB=15.9333;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1206;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=570;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=35.5824;SRR=0;TYPE=del;ANN=CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817delT|p.Leu3606fs|10817/21291|10817/21291|3606/7096||,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10817delT|p.Leu3606fs|10817/13218|10817/13218|3606/4405||,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.110delT|p.Leu37fs|110/870|110/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.110delT|p.Leu37fs|110/870|110/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-761delT|||||761|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-761delT|||||761|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1010delT|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1010delT|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1604delT|||||1604|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1604delT|||||1604|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1943delT|||||1943|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1943delT|||||1943|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2360delT|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2360delT|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2528delT|||||2528|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2528delT|||||2528|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1028delT|||||1028|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1028delT|||||1028|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*110delT|||||110|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*110delT|||||110|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:570:1:39:0,-0.919915,-47.7463

-NC_045512.2	11146	.	G	T	173.224	.	AB=0.3125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=10;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=24.725;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.8864;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=385;QR=850;RO=22;RPL=5;RPP=3.0103;RPPR=3.0103;RPR=5;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10881G>T|p.Met3627Ile|10881/21291|10881/21291|3627/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10881G>T|p.Met3627Ile|10881/13218|10881/13218|3627/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.174G>T|p.Met58Ile|174/870|174/870|58/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.174G>T|p.Met58Ile|174/870|174/870|58/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-697G>T|||||697|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-697G>T|||||697|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-946G>T|||||946|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-946G>T|||||946|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1540G>T|||||1540|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1540G>T|||||1540|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1879G>T|||||1879|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1879G>T|||||1879|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2296G>T|||||2296|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2296G>T|||||2296|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2592G>T|||||2592|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2592G>T|||||2592|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1092G>T|||||1092|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1092G>T|||||1092|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*174G>T|||||174|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*174G>T|||||174|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:32:22,10:22:850:10:385:-25.3739,0,-67.1901

-NC_045512.2	11194	.	T	C	1.52189E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=7.35324;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.7027;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1167;RO=30;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10929T>C|p.Ser3643Ser|10929/21291|10929/21291|3643/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10929T>C|p.Ser3643Ser|10929/13218|10929/13218|3643/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.222T>C|p.Ser74Ser|222/870|222/870|74/289||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.222T>C|p.Ser74Ser|222/870|222/870|74/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-649T>C|||||649|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-649T>C|||||649|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-898T>C|||||898|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-898T>C|||||898|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1492T>C|||||1492|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1492T>C|||||1492|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1831T>C|||||1831|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1831T>C|||||1831|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2248T>C|||||2248|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2248T>C|||||2248|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2640T>C|||||2640|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2640T>C|||||2640|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1140T>C|||||1140|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1140T>C|||||1140|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*222T>C|||||222|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*222T>C|||||222|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:30,2:30:1167:2:77:0,-2.32382,-98.0185

-NC_045512.2	11248	.	GC	AA	3.93418E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.2536;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1138;RO=30;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=complex;ANN=AA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10983_10984delGCinsAA|p.MetArg3661IleSer|10983/21291|10983/21291|3661/7096||,AA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10983_10984delGCinsAA|p.MetArg3661IleSer|10983/13218|10983/13218|3661/4405||,AA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.276_277delGCinsAA|p.MetArg92IleSer|276/870|276/870|92/289||WARNING_TRANSCRIPT_NO_START_CODON,AA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.276_277delGCinsAA|p.MetArg92IleSer|276/870|276/870|92/289||WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-595_-594delGCinsAA|||||595|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-595_-594delGCinsAA|||||595|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-844_-843delGCinsAA|||||844|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-844_-843delGCinsAA|||||844|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1438_-1437delGCinsAA|||||1438|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1438_-1437delGCinsAA|||||1438|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1777_-1776delGCinsAA|||||1777|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1777_-1776delGCinsAA|||||1777|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2194_-2193delGCinsAA|||||2194|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2194_-2193delGCinsAA|||||2194|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4989_-4988delGCinsAA|||||4989|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2694_*2695delGCinsAA|||||2694|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2694_*2695delGCinsAA|||||2694|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1194_*1195delGCinsAA|||||1194|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1194_*1195delGCinsAA|||||1194|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*276_*277delGCinsAA|||||276|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*276_*277delGCinsAA|||||276|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1138:1:39:0,-5.43537,-98.8296

-NC_045512.2	11310	.	G	C	1.48795E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.7944;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=690;RO=18;RPL=0;RPP=5.18177;RPPR=26.6552;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=26.6552;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11045G>C|p.Cys3682Ser|11045/21291|11045/21291|3682/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11045G>C|p.Cys3682Ser|11045/13218|11045/13218|3682/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.338G>C|p.Cys113Ser|338/870|338/870|113/289||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.338G>C|p.Cys113Ser|338/870|338/870|113/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-533G>C|||||533|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-533G>C|||||533|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-782G>C|||||782|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-782G>C|||||782|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1376G>C|||||1376|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1376G>C|||||1376|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1715G>C|||||1715|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1715G>C|||||1715|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2132G>C|||||2132|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2132G>C|||||2132|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4927G>C|||||4927|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2756G>C|||||2756|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2756G>C|||||2756|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1256G>C|||||1256|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1256G>C|||||1256|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*338G>C|||||338|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*338G>C|||||338|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:690:1:36:0,-2.12129,-58.8337

-NC_045512.2	11533	.	A	G	79.3239	.	AB=0.666667;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=11.6962;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=4.05965;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=78;RO=2;RPL=2;RPP=3.0103;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11268A>G|p.Arg3756Arg|11268/21291|11268/21291|3756/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11268A>G|p.Arg3756Arg|11268/13218|11268/13218|3756/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.561A>G|p.Arg187Arg|561/870|561/870|187/289||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.561A>G|p.Arg187Arg|561/870|561/870|187/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-310A>G|||||310|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-310A>G|||||310|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-559A>G|||||559|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-559A>G|||||559|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1153A>G|||||1153|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1153A>G|||||1153|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1492A>G|||||1492|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1492A>G|||||1492|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1909A>G|||||1909|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1909A>G|||||1909|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4704A>G|||||4704|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2979A>G|||||2979|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2979A>G|||||2979|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1479A>G|||||1479|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1479A>G|||||1479|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*561A>G|||||561|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*561A>G|||||561|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:2,4:2:78:4:156:-12.6111,0,-5.59729

-NC_045512.2	11557	.	G	A	2.97837E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.4031;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=601;RO=18;RPL=0;RPP=5.18177;RPPR=42.0968;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=20.3821;SRR=3;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11292G>A|p.Glu3764Glu|11292/21291|11292/21291|3764/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11292G>A|p.Glu3764Glu|11292/13218|11292/13218|3764/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.585G>A|p.Glu195Glu|585/870|585/870|195/289||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.585G>A|p.Glu195Glu|585/870|585/870|195/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-286G>A|||||286|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-286G>A|||||286|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-535G>A|||||535|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-535G>A|||||535|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1129G>A|||||1129|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1129G>A|||||1129|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1468G>A|||||1468|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1468G>A|||||1468|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1885G>A|||||1885|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1885G>A|||||1885|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4680G>A|||||4680|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3003G>A|||||3003|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3003G>A|||||3003|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1503G>A|||||1503|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1503G>A|||||1503|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*585G>A|||||585|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*585G>A|||||585|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:601:1:29:0,-2.81991,-51.5061

-NC_045512.2	11588	.	A	T	2.08236E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.3774;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=770;RO=20;RPL=1;RPP=5.18177;RPPR=30.8051;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=30.8051;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11323A>T|p.Thr3775Ser|11323/21291|11323/21291|3775/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11323A>T|p.Thr3775Ser|11323/13218|11323/13218|3775/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.616A>T|p.Thr206Ser|616/870|616/870|206/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.616A>T|p.Thr206Ser|616/870|616/870|206/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-255A>T|||||255|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-255A>T|||||255|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-504A>T|||||504|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-504A>T|||||504|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1098A>T|||||1098|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1098A>T|||||1098|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1437A>T|||||1437|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1437A>T|||||1437|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1854A>T|||||1854|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1854A>T|||||1854|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4649A>T|||||4649|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3034A>T|||||3034|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3034A>T|||||3034|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1534A>T|||||1534|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1534A>T|||||1534|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*616A>T|||||616|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*616A>T|||||616|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:770:1:19:0,-4.42166,-67.7284

-NC_045512.2	11673	.	A	G	1.11413E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=34.9902;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.6904;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=834;RO=22;RPL=0;RPP=5.18177;RPPR=28.2783;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=17.2236;SRR=5;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11408A>G|p.Tyr3803Cys|11408/21291|11408/21291|3803/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11408A>G|p.Tyr3803Cys|11408/13218|11408/13218|3803/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.701A>G|p.Tyr234Cys|701/870|701/870|234/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.701A>G|p.Tyr234Cys|701/870|701/870|234/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-170A>G|||||170|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-170A>G|||||170|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-419A>G|||||419|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-419A>G|||||419|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1013A>G|||||1013|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1013A>G|||||1013|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1352A>G|||||1352|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1352A>G|||||1352|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1769A>G|||||1769|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1769A>G|||||1769|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4564A>G|||||4564|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3119A>G|||||3119|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3119A>G|||||3119|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1619A>G|||||1619|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1619A>G|||||1619|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*701A>G|||||701|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*701A>G|||||701|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:834:1:38:0,-3.12642,-71.5881

-NC_045512.2	11687	.	C	T	1.98744E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=43.4331;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.4439;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=982;RO=26;RPL=1;RPP=5.18177;RPPR=15.0369;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=8.35546;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11422C>T|p.Leu3808Phe|11422/21291|11422/21291|3808/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11422C>T|p.Leu3808Phe|11422/13218|11422/13218|3808/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.715C>T|p.Leu239Phe|715/870|715/870|239/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.715C>T|p.Leu239Phe|715/870|715/870|239/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-156C>T|||||156|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-156C>T|||||156|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-405C>T|||||405|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-405C>T|||||405|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-999C>T|||||999|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-999C>T|||||999|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1338C>T|||||1338|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1338C>T|||||1338|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1755C>T|||||1755|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1755C>T|||||1755|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4550C>T|||||4550|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3133C>T|||||3133|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3133C>T|||||3133|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1633C>T|||||1633|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1633C>T|||||1633|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*715C>T|||||715|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*715C>T|||||715|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:982:1:19:0,-6.22784,-86.7848

-NC_045512.2	11795	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=62.6327;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.5538;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1347;RO=35;RPL=1;RPP=5.18177;RPPR=3.56868;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11530T>G|p.Leu3844Val|11530/21291|11530/21291|3844/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11530T>G|p.Leu3844Val|11530/13218|11530/13218|3844/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.823T>G|p.Leu275Val|823/870|823/870|275/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.823T>G|p.Leu275Val|823/870|823/870|275/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-48T>G|||||48|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-48T>G|||||48|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-297T>G|||||297|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-297T>G|||||297|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-891T>G|||||891|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-891T>G|||||891|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1230T>G|||||1230|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1230T>G|||||1230|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1647T>G|||||1647|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1647T>G|||||1647|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4442T>G|||||4442|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3241T>G|||||3241|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3241T>G|||||3241|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1741T>G|||||1741|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1741T>G|||||1741|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*823T>G|||||823|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*823T>G|||||823|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1347:1:15:0,-9.33709,-120.016

-NC_045512.2	11813	.	A	T	1.1206E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=6.20364;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.7754;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=661;RO=17;RPL=1;RPP=5.18177;RPPR=6.20364;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=39.9253;SRR=17;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11548A>T|p.Lys3850*|11548/21291|11548/21291|3850/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11548A>T|p.Lys3850*|11548/13218|11548/13218|3850/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.841A>T|p.Lys281*|841/870|841/870|281/289||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.841A>T|p.Lys281*|841/870|841/870|281/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-30A>T|||||30|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-30A>T|||||30|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-279A>T|||||279|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-279A>T|||||279|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-873A>T|||||873|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-873A>T|||||873|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1212A>T|||||1212|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1212A>T|||||1212|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1629A>T|||||1629|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1629A>T|||||1629|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4424A>T|||||4424|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3259A>T|||||3259|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3259A>T|||||3259|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1759A>T|||||1759|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1759A>T|||||1759|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*841A>T|||||841|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*841A>T|||||841|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:661:1:39:0,-1.52198,-55.9306

-NC_045512.2	11834	.	A	G	8.91572E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=652;RO=17;RPL=1;RPP=5.18177;RPPR=39.9253;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=39.9253;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11569A>G|p.Thr3857Ala|11569/21291|11569/21291|3857/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11569A>G|p.Thr3857Ala|11569/13218|11569/13218|3857/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.862A>G|p.Thr288Ala|862/870|862/870|288/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.862A>G|p.Thr288Ala|862/870|862/870|288/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-9A>G|||||9|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-9A>G|||||9|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-258A>G|||||258|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-258A>G|||||258|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-852A>G|||||852|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-852A>G|||||852|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1191A>G|||||1191|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1191A>G|||||1191|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1608A>G|||||1608|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1608A>G|||||1608|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4403A>G|||||4403|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3280A>G|||||3280|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3280A>G|||||3280|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1780A>G|||||1780|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1780A>G|||||1780|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*862A>G|||||862|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*862A>G|||||862|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:652:1:38:0,-1.62127,-55.2183

-NC_045512.2	12117	.	T	C	1.35316E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=3.94093;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.4955;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=785;RO=21;RPL=0;RPP=5.18177;RPPR=40.3389;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11852T>C|p.Leu3951Pro|11852/21291|11852/21291|3951/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11852T>C|p.Leu3951Pro|11852/13218|11852/13218|3951/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.26T>C|p.Leu9Pro|26/594|26/594|9/197||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.26T>C|p.Leu9Pro|26/594|26/594|9/197||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-569T>C|||||569|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-569T>C|||||569|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-908T>C|||||908|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-908T>C|||||908|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1325T>C|||||1325|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1325T>C|||||1325|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4120T>C|||||4120|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3563T>C|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3563T>C|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2063T>C|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2063T>C|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1145T>C|||||1145|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1145T>C|||||1145|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*275T>C|||||275|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*275T>C|||||275|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*26T>C|||||26|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*26T>C|||||26|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:785:1:33:0,-3.32352,-67.6759

-NC_045512.2	12235	.	A	G	1.62526E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=38.1882;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.0087;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=767;RO=20;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11970A>G|p.Glu3990Glu|11970/21291|11970/21291|3990/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11970A>G|p.Glu3990Glu|11970/13218|11970/13218|3990/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.144A>G|p.Glu48Glu|144/594|144/594|48/197||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.144A>G|p.Glu48Glu|144/594|144/594|48/197||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-451A>G|||||451|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-451A>G|||||451|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-790A>G|||||790|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-790A>G|||||790|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1207A>G|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1207A>G|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4002A>G|||||4002|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3681A>G|||||3681|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3681A>G|||||3681|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2181A>G|||||2181|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2181A>G|||||2181|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1263A>G|||||1263|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1263A>G|||||1263|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*393A>G|||||393|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*393A>G|||||393|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*144A>G|||||144|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*144A>G|||||144|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:767:1:38:0,-2.52436,-65.5622

-NC_045512.2	12255	.	T	G	9.19054E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=28.1125;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.6439;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=921;RO=25;RPL=1;RPP=5.18177;RPPR=3.79203;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=5.18177;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11990T>G|p.Met3997Arg|11990/21291|11990/21291|3997/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11990T>G|p.Met3997Arg|11990/13218|11990/13218|3997/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.164T>G|p.Met55Arg|164/594|164/594|55/197||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.164T>G|p.Met55Arg|164/594|164/594|55/197||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-431T>G|||||431|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-431T>G|||||431|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-770T>G|||||770|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-770T>G|||||770|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1187T>G|||||1187|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1187T>G|||||1187|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3982T>G|||||3982|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3701T>G|||||3701|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3701T>G|||||3701|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2201T>G|||||2201|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2201T>G|||||2201|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1283T>G|||||1283|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1283T>G|||||1283|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*413T>G|||||413|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*413T>G|||||413|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*164T>G|||||164|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*164T>G|||||164|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:921:1:34:0,-4.42787,-79.8011

-NC_045512.2	12346	.	T	G	6.6751E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.5287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=766;RO=20;RPL=1;RPP=5.18177;RPPR=3.44459;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12081T>G|p.Ser4027Arg|12081/21291|12081/21291|4027/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12081T>G|p.Ser4027Arg|12081/13218|12081/13218|4027/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.255T>G|p.Ser85Arg|255/594|255/594|85/197||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.255T>G|p.Ser85Arg|255/594|255/594|85/197||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-340T>G|||||340|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-340T>G|||||340|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-679T>G|||||679|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-679T>G|||||679|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1096T>G|||||1096|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1096T>G|||||1096|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3891T>G|||||3891|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3792T>G|||||3792|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3792T>G|||||3792|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2292T>G|||||2292|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2292T>G|||||2292|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1374T>G|||||1374|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1374T>G|||||1374|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*504T>G|||||504|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*504T>G|||||504|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*255T>G|||||255|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*255T>G|||||255|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:766:1:14:0,-4.92164,-67.8644

-NC_045512.2	12433	.	T	C	3.5369E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8373;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=824;RO=22;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12168T>C|p.Cys4056Cys|12168/21291|12168/21291|4056/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12168T>C|p.Cys4056Cys|12168/13218|12168/13218|4056/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.342T>C|p.Cys114Cys|342/594|342/594|114/197||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.342T>C|p.Cys114Cys|342/594|342/594|114/197||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-253T>C|||||253|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-253T>C|||||253|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-592T>C|||||592|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-592T>C|||||592|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1009T>C|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1009T>C|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3804T>C|||||3804|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3879T>C|||||3879|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3879T>C|||||3879|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2379T>C|||||2379|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2379T>C|||||2379|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1461T>C|||||1461|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1461T>C|||||1461|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*591T>C|||||591|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*591T>C|||||591|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*342T>C|||||342|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*342T>C|||||342|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:824:1:33:0,-3.62455,-71.1826

-NC_045512.2	12577	.	A	T	3.64155E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=7.35324;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8099;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=855;RO=22;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12312A>T|p.Ala4104Ala|12312/21291|12312/21291|4104/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12312A>T|p.Ala4104Ala|12312/13218|12312/13218|4104/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.486A>T|p.Ala162Ala|486/594|486/594|162/197||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.486A>T|p.Ala162Ala|486/594|486/594|162/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-109A>T|||||109|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-109A>T|||||109|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-448A>T|||||448|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-448A>T|||||448|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-865A>T|||||865|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-865A>T|||||865|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3660A>T|||||3660|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4023A>T|||||4023|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4023A>T|||||4023|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2523A>T|||||2523|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2523A>T|||||2523|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1605A>T|||||1605|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1605A>T|||||1605|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*735A>T|||||735|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*735A>T|||||735|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*486A>T|||||486|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*486A>T|||||486|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:22,2:22:855:2:33:0,-4.08976,-74.1372

-NC_045512.2	12716	.	C	A	5.93778E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.7131;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=652;RO=18;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=7.35324;SRR=12;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12451C>A|p.Gln4151Lys|12451/21291|12451/21291|4151/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12451C>A|p.Gln4151Lys|12451/13218|12451/13218|4151/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.31C>A|p.Gln11Lys|31/339|31/339|11/112||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.31C>A|p.Gln11Lys|31/339|31/339|11/112||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-309C>A|||||309|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-309C>A|||||309|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-726C>A|||||726|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-726C>A|||||726|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3521C>A|||||3521|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4162C>A|||||4162|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4162C>A|||||4162|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2662C>A|||||2662|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2662C>A|||||2662|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1744C>A|||||1744|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1744C>A|||||1744|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*874C>A|||||874|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*874C>A|||||874|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*625C>A|||||625|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*625C>A|||||625|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*31C>A|||||31|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*31C>A|||||31|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:652:1:32:0,-2.52026,-55.803

-NC_045512.2	12730	.	T	C	1.62526E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.0087;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=760;RO=20;RPL=0;RPP=5.18177;RPPR=4.74748;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=4.74748;SRR=12;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12465T>C|p.Ala4155Ala|12465/21291|12465/21291|4155/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12465T>C|p.Ala4155Ala|12465/13218|12465/13218|4155/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.45T>C|p.Ala15Ala|45/339|45/339|15/112||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.45T>C|p.Ala15Ala|45/339|45/339|15/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-295T>C|||||295|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-295T>C|||||295|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-712T>C|||||712|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-712T>C|||||712|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3507T>C|||||3507|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4176T>C|||||4176|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4176T>C|||||4176|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2676T>C|||||2676|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2676T>C|||||2676|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1758T>C|||||1758|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1758T>C|||||1758|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*888T>C|||||888|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*888T>C|||||888|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*639T>C|||||639|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*639T>C|||||639|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*45T>C|||||45|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*45T>C|||||45|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:760:1:38:0,-2.52436,-64.9333

-NC_045512.2	12747	.	C	T	2.71476	.	AB=0.190476;ABP=20.4855;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=11.6962;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.141073;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=662;RO=17;RPL=4;RPP=11.6962;RPPR=3.13803;RPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=9;SRP=3.13803;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12482C>T|p.Thr4161Ile|12482/21291|12482/21291|4161/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12482C>T|p.Thr4161Ile|12482/13218|12482/13218|4161/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.62C>T|p.Thr21Ile|62/339|62/339|21/112||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.62C>T|p.Thr21Ile|62/339|62/339|21/112||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-278C>T|||||278|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-278C>T|||||278|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-695C>T|||||695|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-695C>T|||||695|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3490C>T|||||3490|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4193C>T|||||4193|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4193C>T|||||4193|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2693C>T|||||2693|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2693C>T|||||2693|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1775C>T|||||1775|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1775C>T|||||1775|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*905C>T|||||905|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*905C>T|||||905|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*656C>T|||||656|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*656C>T|||||656|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*62C>T|||||62|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*62C>T|||||62|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:17,4:17:662:4:156:-8.09566,0,-53.5955

-NC_045512.2	13014	.	T	G	1.36814E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.053;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1206;RO=34;RPL=0;RPP=5.18177;RPPR=19.3602;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=19.3602;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12749T>G|p.Val4250Gly|12749/21291|12749/21291|4250/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12749T>G|p.Val4250Gly|12749/13218|12749/13218|4250/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.329T>G|p.Val110Gly|329/339|329/339|110/112||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.329T>G|p.Val110Gly|329/339|329/339|110/112||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-11T>G|||||11|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-11T>G|||||11|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-428T>G|||||428|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-428T>G|||||428|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3223T>G|||||3223|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4460T>G|||||4460|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4460T>G|||||4460|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2960T>G|||||2960|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2960T>G|||||2960|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2042T>G|||||2042|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2042T>G|||||2042|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1172T>G|||||1172|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1172T>G|||||1172|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*923T>G|||||923|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*923T>G|||||923|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*329T>G|||||329|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*329T>G|||||329|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:34,1:34:1206:1:33:0,-7.23691,-105.531

-NC_045512.2	13020	.	T	C	2.60717E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.8119;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1368;RO=37;RPL=0;RPP=5.18177;RPPR=24.1968;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=24.1968;SRR=9;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12755T>C|p.Leu4252Pro|12755/21291|12755/21291|4252/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12755T>C|p.Leu4252Pro|12755/13218|12755/13218|4252/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.335T>C|p.Leu112Pro|335/339|335/339|112/112||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.335T>C|p.Leu112Pro|335/339|335/339|112/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-5T>C|||||5|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-5T>C|||||5|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-422T>C|||||422|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-422T>C|||||422|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3217T>C|||||3217|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4466T>C|||||4466|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4466T>C|||||4466|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2966T>C|||||2966|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2966T>C|||||2966|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2048T>C|||||2048|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2048T>C|||||2048|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1178T>C|||||1178|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1178T>C|||||1178|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*929T>C|||||929|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*929T>C|||||929|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*335T>C|||||335|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*335T>C|||||335|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1368:1:17:0,-9.73916,-121.706

-NC_045512.2	13034	.	GCA	GA	6.2985E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=38;DPB=37.6667;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.9827;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1416;RO=37;RPL=0;RPP=5.18177;RPPR=24.1968;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=24.1968;SRR=9;TYPE=del;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12770delC|p.Ala4257fs|12770/21291|12770/21291|4257/7096||,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12770delC|p.Ala4257fs|12770/13218|12770/13218|4257/4405||,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.11delC|p.Ala4fs|11/417|11/417|4/138||WARNING_TRANSCRIPT_NO_START_CODON,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.11delC|p.Ala4fs|11/417|11/417|4/138||WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-407delC|||||407|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-407delC|||||407|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3202delC|||||3202|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4481delC|||||4481|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4481delC|||||4481|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2981delC|||||2981|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2981delC|||||2981|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2063delC|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2063delC|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1193delC|||||1193|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1193delC|||||1193|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*944delC|||||944|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*944delC|||||944|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*350delC|||||350|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*350delC|||||350|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*11delC|||||11|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*11delC|||||11|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1416:1:38:0,-7.64187,-123.922

-NC_045512.2	13043	.	G	T	1.507E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.754;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1437;RO=37;RPL=0;RPP=5.18177;RPPR=24.1968;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=24.1968;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12778G>T|p.Val4260Leu|12778/21291|12778/21291|4260/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12778G>T|p.Val4260Leu|12778/13218|12778/13218|4260/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.19G>T|p.Val7Leu|19/417|19/417|7/138||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.19G>T|p.Val7Leu|19/417|19/417|7/138||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-399G>T|||||399|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-399G>T|||||399|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3194G>T|||||3194|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4997G>T|||||4997|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4489G>T|||||4489|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4489G>T|||||4489|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2989G>T|||||2989|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2989G>T|||||2989|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2071G>T|||||2071|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2071G>T|||||2071|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1201G>T|||||1201|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1201G>T|||||1201|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*952G>T|||||952|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*952G>T|||||952|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*358G>T|||||358|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*358G>T|||||358|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*19G>T|||||19|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*19G>T|||||19|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1437:1:39:0,-7.54258,-125.711

-NC_045512.2	13083	.	CTG	CTTG	6.2985E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=38;DPB=38.3333;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.9827;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1420;RO=37;RPL=1;RPP=5.18177;RPPR=28.8919;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=29;SRP=28.8919;SRR=8;TYPE=ins;ANN=CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12819dupT|p.Val4274fs|12820/21291|12820/21291|4274/7096||,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12819dupT|p.Val4274fs|12820/13218|12820/13218|4274/4405||,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.60dupT|p.Val21fs|61/417|61/417|21/138||WARNING_TRANSCRIPT_NO_START_CODON,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.60dupT|p.Val21fs|61/417|61/417|21/138||WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-358dupT|||||357|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-358dupT|||||357|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3153dupT|||||3152|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4956dupT|||||4955|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4530dupT|||||4531|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4530dupT|||||4531|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3030dupT|||||3031|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3030dupT|||||3031|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2112dupT|||||2113|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2112dupT|||||2113|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1242dupT|||||1243|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1242dupT|||||1243|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*993dupT|||||994|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*993dupT|||||994|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*399dupT|||||400|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*399dupT|||||400|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*60dupT|||||61|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*60dupT|||||61|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1420:1:38:0,-7.64187,-124.285

-NC_045512.2	13091	.	G	A	1.507E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.754;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1413;RO=37;RPL=0;RPP=5.18177;RPPR=24.1968;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=24.1968;SRR=9;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12826G>A|p.Ala4276Thr|12826/21291|12826/21291|4276/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12826G>A|p.Ala4276Thr|12826/13218|12826/13218|4276/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.67G>A|p.Ala23Thr|67/417|67/417|23/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.67G>A|p.Ala23Thr|67/417|67/417|23/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-351G>A|||||351|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-351G>A|||||351|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3146G>A|||||3146|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4949G>A|||||4949|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4537G>A|||||4537|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4537G>A|||||4537|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3037G>A|||||3037|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3037G>A|||||3037|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2119G>A|||||2119|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2119G>A|||||2119|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1249G>A|||||1249|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1249G>A|||||1249|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1000G>A|||||1000|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1000G>A|||||1000|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*406G>A|||||406|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*406G>A|||||406|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*67G>A|||||67|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*67G>A|||||67|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1413:1:39:0,-7.54258,-123.555

-NC_045512.2	13372	.	CTG	CTTG	1.66952E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=32;DPB=32.3333;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.8368;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1123;RO=31;RPL=1;RPP=5.18177;RPPR=46.79;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=46.79;SRR=28;TYPE=ins;ANN=CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13108dupT|p.Cys4370fs|13109/21291|13109/21291|4370/7096||,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.13108dupT|p.Cys4370fs|13109/13218|13109/13218|4370/4405||,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.349dupT|p.Cys117fs|350/417|350/417|117/138||WARNING_TRANSCRIPT_NO_START_CODON,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.349dupT|p.Cys117fs|350/417|350/417|117/138||WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-69dupT|||||68|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-69dupT|||||68|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2864dupT|||||2863|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4667dupT|||||4666|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4819dupT|||||4820|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4819dupT|||||4820|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3319dupT|||||3320|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3319dupT|||||3320|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2401dupT|||||2402|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2401dupT|||||2402|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1531dupT|||||1532|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1531dupT|||||1532|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1282dupT|||||1283|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1282dupT|||||1283|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*688dupT|||||689|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*688dupT|||||689|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*349dupT|||||350|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*349dupT|||||350|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1123:1:38:0,-5.83569,-97.5815

-NC_045512.2	13382	.	T	A	2.16978E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.5056;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1013;RO=29;RPL=1;RPP=5.18177;RPPR=42.621;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=42.621;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13117T>A|p.Cys4373Ser|13117/21291|13117/21291|4373/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.13117T>A|p.Cys4373Ser|13117/13218|13117/13218|4373/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.358T>A|p.Cys120Ser|358/417|358/417|120/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.358T>A|p.Cys120Ser|358/417|358/417|120/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-60T>A|||||60|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-60T>A|||||60|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2855T>A|||||2855|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4658T>A|||||4658|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4828T>A|||||4828|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4828T>A|||||4828|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3328T>A|||||3328|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3328T>A|||||3328|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2410T>A|||||2410|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2410T>A|||||2410|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1540T>A|||||1540|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1540T>A|||||1540|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1291T>A|||||1291|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1291T>A|||||1291|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*697T>A|||||697|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*697T>A|||||697|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*358T>A|||||358|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*358T>A|||||358|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1013:1:32:0,-5.83159,-88.28

-NC_045512.2	13384	.	C	G	4.479E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.6076;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=774;RO=22;RPL=1;RPP=5.18177;RPPR=28.2783;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=28.2783;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13119C>G|p.Cys4373Trp|13119/21291|13119/21291|4373/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.13119C>G|p.Cys4373Trp|13119/13218|13119/13218|4373/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.360C>G|p.Cys120Trp|360/417|360/417|120/138||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.360C>G|p.Cys120Trp|360/417|360/417|120/138||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-58C>G|||||58|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-58C>G|||||58|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2853C>G|||||2853|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4656C>G|||||4656|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4830C>G|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4830C>G|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3330C>G|||||3330|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3330C>G|||||3330|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2412C>G|||||2412|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2412C>G|||||2412|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1542C>G|||||1542|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1542C>G|||||1542|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1293C>G|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1293C>G|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*699C>G|||||699|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*699C>G|||||699|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*360C>G|||||360|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*360C>G|||||360|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:774:1:34:0,-3.52478,-66.5807

-NC_045512.2	13607	.	TCCAA	TCAA	2.15768E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=28;DPB=27.8;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.1111;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=939;RO=27;RPL=0;RPP=5.18177;RPPR=38.4777;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=38.4777;SRR=3;TYPE=del;ANN=TCAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13345delC|p.Gln4449fs|13345/21291|13345/21291|4449/7096||,TCAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.169delC|p.Gln57fs|169/2796|169/2796|57/931||WARNING_TRANSCRIPT_NO_START_CODON,TCAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2628delC|||||2628|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4431delC|||||4431|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*126delC|||||126|,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3555delC|||||3555|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3555delC|||||3555|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2637delC|||||2637|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2637delC|||||2637|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1767delC|||||1767|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1767delC|||||1767|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1518delC|||||1518|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1518delC|||||1518|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*924delC|||||924|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*924delC|||||924|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*585delC|||||585|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*585delC|||||585|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*168delC|||||168|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*168delC|||||168|WARNING_TRANSCRIPT_NO_START_CODON,TCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*129delC|||||129|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:939:1:34:0,-5.02993,-81.376

-NC_045512.2	13643	.	C	G	2.91109E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.1111;NS=1;NUMALT=1;ODDS=33.1965;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1052;RO=27;RPL=0;RPP=5.18177;RPPR=38.4777;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=38.4777;SRR=3;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13379C>G|p.Ser4460Cys|13379/21291|13379/21291|4460/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.203C>G|p.Ser68Cys|203/2796|203/2796|68/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2594C>G|||||2594|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4397C>G|||||4397|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*160C>G|||||160|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3589C>G|||||3589|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3589C>G|||||3589|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2671C>G|||||2671|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2671C>G|||||2671|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1801C>G|||||1801|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1801C>G|||||1801|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1552C>G|||||1552|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1552C>G|||||1552|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*958C>G|||||958|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*958C>G|||||958|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*619C>G|||||619|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*619C>G|||||619|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*202C>G|||||202|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*202C>G|||||202|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*163C>G|||||163|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1052:1:39:0,-4.53228,-91.003

-NC_045512.2	13658	.	A	G	2.1004E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.1111;NS=1;NUMALT=1;ODDS=37.5636;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1052;RO=27;RPL=0;RPP=5.18177;RPPR=38.4777;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=38.4777;SRR=3;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13394A>G|p.Lys4465Arg|13394/21291|13394/21291|4465/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.218A>G|p.Lys73Arg|218/2796|218/2796|73/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2579A>G|||||2579|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4382A>G|||||4382|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*175A>G|||||175|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3604A>G|||||3604|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3604A>G|||||3604|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2686A>G|||||2686|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2686A>G|||||2686|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1816A>G|||||1816|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1816A>G|||||1816|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1567A>G|||||1567|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1567A>G|||||1567|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*973A>G|||||973|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*973A>G|||||973|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*634A>G|||||634|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*634A>G|||||634|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*217A>G|||||217|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*217A>G|||||217|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*178A>G|||||178|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1052:1:20:0,-6.42888,-92.8996

-NC_045512.2	13672	.	TCT	TCCT	3.39026E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=28;DPB=28.3333;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.1111;NS=1;NUMALT=1;ODDS=33.4251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1045;RO=27;RPL=1;RPP=5.18177;RPPR=45.5551;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=45.5551;SRR=2;TYPE=ins;ANN=TCCT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13409dupC|p.Asn4471fs|13410/21291|13410/21291|4470/7096||,TCCT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.233dupC|p.Asn79fs|234/2796|234/2796|78/931||WARNING_TRANSCRIPT_NO_START_CODON,TCCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2564dupC|||||2563|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4367dupC|||||4366|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*190dupC|||||191|,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3619dupC|||||3620|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3619dupC|||||3620|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2701dupC|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2701dupC|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1831dupC|||||1832|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1831dupC|||||1832|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1582dupC|||||1583|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1582dupC|||||1583|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*988dupC|||||989|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*988dupC|||||989|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*649dupC|||||650|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*649dupC|||||650|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*232dupC|||||233|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*232dupC|||||233|WARNING_TRANSCRIPT_NO_START_CODON,TCCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*193dupC|||||194|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1045:1:38:0,-4.63157,-90.4739

-NC_045512.2	13735	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.5;NS=1;NUMALT=1;ODDS=67.2674;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1828;RO=48;RPL=0;RPP=5.18177;RPPR=3.19126;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13471C>T|p.His4491Tyr|13471/21291|13471/21291|4491/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.295C>T|p.His99Tyr|295/2796|295/2796|99/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2502C>T|||||2502|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4305C>T|||||4305|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*252C>T|||||252|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3681C>T|||||3681|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3681C>T|||||3681|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2763C>T|||||2763|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2763C>T|||||2763|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1893C>T|||||1893|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1893C>T|||||1893|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1644C>T|||||1644|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1644C>T|||||1644|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1050C>T|||||1050|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1050C>T|||||1050|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*711C>T|||||711|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*711C>T|||||711|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*294C>T|||||294|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*294C>T|||||294|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*255C>T|||||255|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:49:48,1:48:1828:1:15:0,-13.2505,-163.181

-NC_045512.2	13774	.	C	T	575.99	.	AB=0.489796;ABP=3.05462;AC=1;AF=0.5;AN=2;AO=24;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=55.1256;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=59;MQMR=60;NS=1;NUMALT=1;ODDS=132.627;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=932;QR=950;RO=25;RPL=12;RPP=3.0103;RPPR=3.09716;RPR=12;RUN=1;SAF=12;SAP=3.0103;SAR=12;SRF=13;SRP=3.09716;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13510C>T|p.Pro4504Ser|13510/21291|13510/21291|4504/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.334C>T|p.Pro112Ser|334/2796|334/2796|112/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2463C>T|||||2463|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4266C>T|||||4266|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*291C>T|||||291|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3720C>T|||||3720|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3720C>T|||||3720|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2802C>T|||||2802|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2802C>T|||||2802|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1932C>T|||||1932|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1932C>T|||||1932|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1683C>T|||||1683|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1683C>T|||||1683|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1089C>T|||||1089|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1089C>T|||||1089|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*750C>T|||||750|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*750C>T|||||750|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*333C>T|||||333|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*333C>T|||||333|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*294C>T|||||294|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:49:25,24:25:950:24:932:-69.3588,0,-71.0603

-NC_045512.2	13896	.	T	A	2.30043E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.2631;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=894;RO=23;RPL=1;RPP=5.18177;RPPR=52.9542;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=52.9542;SRR=23;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13632T>A|p.Cys4544*|13632/21291|13632/21291|4544/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.456T>A|p.Cys152*|456/2796|456/2796|152/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2341T>A|||||2341|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4144T>A|||||4144|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*413T>A|||||413|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3842T>A|||||3842|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3842T>A|||||3842|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2924T>A|||||2924|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2924T>A|||||2924|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2054T>A|||||2054|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2054T>A|||||2054|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1805T>A|||||1805|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1805T>A|||||1805|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1211T>A|||||1211|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1211T>A|||||1211|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*872T>A|||||872|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*872T>A|||||872|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*455T>A|||||455|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*455T>A|||||455|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*416T>A|||||416|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:894:1:37:0,-3.52689,-77.0812

-NC_045512.2	13924	.	TGGTA	TGTA	1.3531E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=44;DPB=43.8;DPRA=0;EPP=5.18177;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.3008;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1594;RO=43;RPL=0;RPP=5.18177;RPPR=4.27278;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=4.27278;SRR=24;TYPE=del;ANN=TGTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13662delG|p.Trp4554fs|13662/21291|13662/21291|4554/7096||,TGTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.486delG|p.Trp162fs|486/2796|486/2796|162/931||WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2311delG|||||2311|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4114delG|||||4114|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*443delG|||||443|,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3872delG|||||3872|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3872delG|||||3872|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2954delG|||||2954|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2954delG|||||2954|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2084delG|||||2084|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2084delG|||||2084|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1835delG|||||1835|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1835delG|||||1835|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1241delG|||||1241|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1241delG|||||1241|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*902delG|||||902|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*902delG|||||902|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*485delG|||||485|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*485delG|||||485|WARNING_TRANSCRIPT_NO_START_CODON,TGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*446delG|||||446|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1594:1:33:0,-9.94618,-140.437

-NC_045512.2	14252	.	T	C	4.94241E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.1144;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1473;RO=38;RPL=1;RPP=5.18177;RPPR=3.9246;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.9246;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13988T>C|p.Leu4663Ser|13988/21291|13988/21291|4663/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.812T>C|p.Leu271Ser|812/2796|812/2796|271/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1985T>C|||||1985|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3788T>C|||||3788|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*769T>C|||||769|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4198T>C|||||4198|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4198T>C|||||4198|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3280T>C|||||3280|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3280T>C|||||3280|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2410T>C|||||2410|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2410T>C|||||2410|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2161T>C|||||2161|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2161T>C|||||2161|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1567T>C|||||1567|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1567T>C|||||1567|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1228T>C|||||1228|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1228T>C|||||1228|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*811T>C|||||811|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*811T>C|||||811|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*772T>C|||||772|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1473:1:39:0,-7.84361,-128.948

-NC_045512.2	14259	.	T	A	1.14669E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.2512;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1475;RO=38;RPL=1;RPP=5.18177;RPPR=3.9246;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.9246;SRR=21;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13995T>A|p.Tyr4665*|13995/21291|13995/21291|4665/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.819T>A|p.Tyr273*|819/2796|819/2796|273/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1978T>A|||||1978|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3781T>A|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*776T>A|||||776|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4205T>A|||||4205|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4205T>A|||||4205|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3287T>A|||||3287|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3287T>A|||||3287|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2417T>A|||||2417|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2417T>A|||||2417|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2168T>A|||||2168|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2168T>A|||||2168|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1574T>A|||||1574|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1574T>A|||||1574|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1235T>A|||||1235|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1235T>A|||||1235|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*818T>A|||||818|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*818T>A|||||818|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*779T>A|||||779|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1475:1:21:0,-9.64022,-130.924

-NC_045512.2	14362	.	C	T	2.88568E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=5.18177;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.8384;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1279;RO=33;RPL=0;RPP=5.18177;RPPR=3.0761;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.0761;SRR=16;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14098C>T|p.Leu4700Leu|14098/21291|14098/21291|4700/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.922C>T|p.Leu308Leu|922/2796|922/2796|308/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1875C>T|||||1875|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3678C>T|||||3678|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*879C>T|||||879|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4308C>T|||||4308|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4308C>T|||||4308|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3390C>T|||||3390|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3390C>T|||||3390|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2520C>T|||||2520|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2520C>T|||||2520|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2271C>T|||||2271|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2271C>T|||||2271|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1677C>T|||||1677|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1677C>T|||||1677|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1338C>T|||||1338|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1338C>T|||||1338|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*921C>T|||||921|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*921C>T|||||921|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*882C>T|||||882|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:33,1:33:1279:1:15:0,-8.73503,-113.9

-NC_045512.2	14408	.	C	T	1065.78	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=34;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=76.8404;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=51.7392;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1314;QR=0;RO=0;RPL=17;RPP=3.0103;RPPR=0;RPR=17;RUN=1;SAF=17;SAP=3.0103;SAR=17;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144C>T|p.Pro4715Leu|14144/21291|14144/21291|4715/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.968C>T|p.Pro323Leu|968/2796|968/2796|323/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1829C>T|||||1829|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3632C>T|||||3632|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*925C>T|||||925|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4354C>T|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4354C>T|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3436C>T|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3436C>T|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2566C>T|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2566C>T|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2317C>T|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2317C>T|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1723C>T|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1723C>T|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1384C>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1384C>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*928C>T|||||928|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:34:0,34:0:0:34:1314:-118.547,-10.235,0

-NC_045512.2	14415	.	T	A	2.88568E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=5.18177;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.8384;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1253;RO=33;RPL=1;RPP=5.18177;RPPR=3.0761;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14151T>A|p.Ser4717Arg|14151/21291|14151/21291|4717/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.975T>A|p.Ser325Arg|975/2796|975/2796|325/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1822T>A|||||1822|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3625T>A|||||3625|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*932T>A|||||932|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4361T>A|||||4361|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4361T>A|||||4361|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3443T>A|||||3443|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3443T>A|||||3443|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2573T>A|||||2573|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2573T>A|||||2573|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2324T>A|||||2324|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2324T>A|||||2324|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1730T>A|||||1730|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1730T>A|||||1730|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1391T>A|||||1391|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1391T>A|||||1391|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*974T>A|||||974|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*974T>A|||||974|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*935T>A|||||935|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:33,1:33:1253:1:15:0,-8.73503,-111.555

-NC_045512.2	14460	.	T	A	8.34447E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.7498;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=852;RO=22;RPL=0;RPP=5.18177;RPPR=12.8806;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=12.8806;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14196T>A|p.Phe4732Leu|14196/21291|14196/21291|4732/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1020T>A|p.Phe340Leu|1020/2796|1020/2796|340/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1777T>A|||||1777|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3580T>A|||||3580|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*977T>A|||||977|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4406T>A|||||4406|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4406T>A|||||4406|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3488T>A|||||3488|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3488T>A|||||3488|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2618T>A|||||2618|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2618T>A|||||2618|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2369T>A|||||2369|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2369T>A|||||2369|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1775T>A|||||1775|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1775T>A|||||1775|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1436T>A|||||1436|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1436T>A|||||1436|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1019T>A|||||1019|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1019T>A|||||1019|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*980T>A|||||980|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:852:1:16:0,-5.32371,-75.4017

-NC_045512.2	14472	.	T	A	7.12637E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=3.13803;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.8332;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=663;RO=17;RPL=1;RPP=5.18177;RPPR=3.13803;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=31.7504;SRR=16;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14208T>A|p.Thr4736Thr|14208/21291|14208/21291|4736/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1032T>A|p.Thr344Thr|1032/2796|1032/2796|344/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1765T>A|||||1765|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3568T>A|||||3568|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*989T>A|||||989|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4418T>A|||||4418|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4418T>A|||||4418|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3500T>A|||||3500|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3500T>A|||||3500|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2630T>A|||||2630|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2630T>A|||||2630|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2381T>A|||||2381|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2381T>A|||||2381|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1787T>A|||||1787|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1787T>A|||||1787|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1448T>A|||||1448|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1448T>A|||||1448|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1031T>A|||||1031|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1031T>A|||||1031|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*992T>A|||||992|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:663:1:17:0,-3.71856,-58.3071

-NC_045512.2	14502	.	A	T	2.69233E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.5041;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=602;RO=16;RPL=1;RPP=5.18177;RPPR=37.7539;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=37.7539;SRR=16;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14238A>T|p.Val4746Val|14238/21291|14238/21291|4746/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1062A>T|p.Val354Val|1062/2796|1062/2796|354/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1735A>T|||||1735|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3538A>T|||||3538|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1019A>T|||||1019|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4448A>T|||||4448|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4448A>T|||||4448|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3530A>T|||||3530|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3530A>T|||||3530|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2660A>T|||||2660|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2660A>T|||||2660|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2411A>T|||||2411|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2411A>T|||||2411|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1817A>T|||||1817|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1817A>T|||||1817|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1478A>T|||||1478|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1478A>T|||||1478|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1061A>T|||||1061|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1061A>T|||||1061|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1022A>T|||||1022|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:602:1:17:0,-3.41753,-52.8095

-NC_045512.2	14535	.	A	T	2.13835E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.7343;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=597;RO=16;RPL=1;RPP=5.18177;RPPR=37.7539;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=37.7539;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14271A>T|p.Arg4757Ser|14271/21291|14271/21291|4757/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1095A>T|p.Arg365Ser|1095/2796|1095/2796|365/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1702A>T|||||1702|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3505A>T|||||3505|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1052A>T|||||1052|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4481A>T|||||4481|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4481A>T|||||4481|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3563A>T|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3563A>T|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2693A>T|||||2693|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2693A>T|||||2693|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2444A>T|||||2444|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2444A>T|||||2444|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1850A>T|||||1850|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1850A>T|||||1850|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1511A>T|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1511A>T|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1094A>T|||||1094|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1094A>T|||||1094|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1055A>T|||||1055|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:597:1:16:0,-3.51753,-52.4591

-NC_045512.2	14657	.	C	A	1.26801E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.3492;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=584;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=35.5824;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14393C>A|p.Ala4798Asp|14393/21291|14393/21291|4798/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1217C>A|p.Ala406Asp|1217/2796|1217/2796|406/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1580C>A|||||1580|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3383C>A|||||3383|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4964C>A|||||4964|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1174C>A|||||1174|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4603C>A|||||4603|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4603C>A|||||4603|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3685C>A|||||3685|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3685C>A|||||3685|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2815C>A|||||2815|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2815C>A|||||2815|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2566C>A|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2566C>A|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1972C>A|||||1972|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1972C>A|||||1972|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1633C>A|||||1633|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1633C>A|||||1633|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1216C>A|||||1216|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1216C>A|||||1216|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1177C>A|||||1177|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:584:1:38:0,-1.01921,-49.106

-NC_045512.2	14710	.	G	C	33.0614	.	AB=0.1875;ABP=30.1537;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=16.0391;EPPR=51.1168;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.61217;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=234;QR=1010;RO=26;RPL=3;RPP=3.0103;RPPR=3.34437;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14446G>C|p.Val4816Leu|14446/21291|14446/21291|4816/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1270G>C|p.Val424Leu|1270/2796|1270/2796|424/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1527G>C|||||1527|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3330G>C|||||3330|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4911G>C|||||4911|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1227G>C|||||1227|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4656G>C|||||4656|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4656G>C|||||4656|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3738G>C|||||3738|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3738G>C|||||3738|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2868G>C|||||2868|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2868G>C|||||2868|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2619G>C|||||2619|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2619G>C|||||2619|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2025G>C|||||2025|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2025G>C|||||2025|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1686G>C|||||1686|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1686G>C|||||1686|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1269G>C|||||1269|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1269G>C|||||1269|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1230G>C|||||1230|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:32:26,6:26:1010:6:234:-11.7981,0,-81.5772

-NC_045512.2	14794	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.1264;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1193;RO=31;RPL=1;RPP=5.18177;RPPR=3.08035;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14530G>A|p.Asp4844Asn|14530/21291|14530/21291|4844/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1354G>A|p.Asp452Asn|1354/2796|1354/2796|452/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1443G>A|||||1443|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3246G>A|||||3246|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4827G>A|||||4827|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1311G>A|||||1311|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4740G>A|||||4740|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4740G>A|||||4740|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3822G>A|||||3822|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3822G>A|||||3822|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2952G>A|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2952G>A|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2703G>A|||||2703|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2703G>A|||||2703|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2109G>A|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2109G>A|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1770G>A|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1770G>A|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1353G>A|||||1353|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1353G>A|||||1353|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1314G>A|||||1314|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1193:1:15:0,-8.13297,-106.169

-NC_045512.2	14805	.	C	T	8.91572E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=24.5973;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=646;RO=17;RPL=1;RPP=5.18177;RPPR=39.9253;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=24.5973;SRR=15;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14541C>T|p.Tyr4847Tyr|14541/21291|14541/21291|4847/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1365C>T|p.Tyr455Tyr|1365/2796|1365/2796|455/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1432C>T|||||1432|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3235C>T|||||3235|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4816C>T|||||4816|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1322C>T|||||1322|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4751C>T|||||4751|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4751C>T|||||4751|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3833C>T|||||3833|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3833C>T|||||3833|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2963C>T|||||2963|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2963C>T|||||2963|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2714C>T|||||2714|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2714C>T|||||2714|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2120C>T|||||2120|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2120C>T|||||2120|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1781C>T|||||1781|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1781C>T|||||1781|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1364C>T|||||1364|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1364C>T|||||1364|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1325C>T|||||1325|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:646:1:38:0,-1.62127,-54.6805

-NC_045512.2	14912	.	A	G	5.93778E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.7131;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=685;RO=18;RPL=1;RPP=5.18177;RPPR=20.3821;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=20.3821;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14648A>G|p.Asn4883Ser|14648/21291|14648/21291|4883/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1472A>G|p.Asn491Ser|1472/2796|1472/2796|491/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1325A>G|||||1325|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3128A>G|||||3128|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4709A>G|||||4709|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1429A>G|||||1429|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4858A>G|||||4858|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4858A>G|||||4858|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3940A>G|||||3940|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3940A>G|||||3940|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3070A>G|||||3070|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3070A>G|||||3070|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2821A>G|||||2821|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2821A>G|||||2821|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2227A>G|||||2227|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2227A>G|||||2227|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1888A>G|||||1888|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1888A>G|||||1888|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1471A>G|||||1471|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1471A>G|||||1471|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1432A>G|||||1432|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:685:1:32:0,-2.52026,-58.7858

-NC_045512.2	15106	.	A	C	1.9974E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.98702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=182;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14842A>C|p.Thr4948Pro|14842/21291|14842/21291|4948/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1666A>C|p.Thr556Pro|1666/2796|1666/2796|556/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1131A>C|||||1131|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2934A>C|||||2934|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4515A>C|||||4515|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1623A>C|||||1623|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4134A>C|||||4134|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4134A>C|||||4134|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3264A>C|||||3264|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3264A>C|||||3264|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3015A>C|||||3015|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3015A>C|||||3015|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2421A>C|||||2421|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2421A>C|||||2421|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2082A>C|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2082A>C|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1665A>C|||||1665|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1665A>C|||||1665|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1626A>C|||||1626|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:182:1:14:0,-0.40619,-15.3344

-NC_045512.2	15176	.	T	A	6.49548E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.926;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=647;RO=20;RPL=0;RPP=5.18177;RPPR=24.2907;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=24.2907;SRR=3;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14912T>A|p.Ile4971Lys|14912/21291|14912/21291|4971/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1736T>A|p.Ile579Lys|1736/2796|1736/2796|579/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1061T>A|||||1061|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2864T>A|||||2864|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4445T>A|||||4445|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1693T>A|||||1693|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4204T>A|||||4204|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4204T>A|||||4204|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3334T>A|||||3334|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3334T>A|||||3334|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3085T>A|||||3085|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3085T>A|||||3085|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2491T>A|||||2491|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2491T>A|||||2491|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2152T>A|||||2152|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2152T>A|||||2152|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1735T>A|||||1735|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1735T>A|||||1735|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1696T>A|||||1696|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:647:1:34:0,-2.92272,-55.1375

-NC_045512.2	15192	.	A	C	3.0467E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.3238;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=876;RO=23;RPL=0;RPP=5.18177;RPPR=30.2953;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=30.2953;SRR=3;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14928A>C|p.Gly4976Gly|14928/21291|14928/21291|4976/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1752A>C|p.Gly584Gly|1752/2796|1752/2796|584/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1045A>C|||||1045|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2848A>C|||||2848|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4429A>C|||||4429|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1709A>C|||||1709|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4220A>C|||||4220|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4220A>C|||||4220|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3350A>C|||||3350|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3350A>C|||||3350|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3101A>C|||||3101|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3101A>C|||||3101|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2507A>C|||||2507|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2507A>C|||||2507|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2168A>C|||||2168|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2168A>C|||||2168|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1751A>C|||||1751|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1751A>C|||||1751|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1712A>C|||||1712|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:876:1:15:0,-5.72473,-77.6628

-NC_045512.2	15261	.	T	A	3.80036E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=40.3389;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.1777;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=791;RO=21;RPL=0;RPP=5.18177;RPPR=48.6112;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=40.3389;SRR=1;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14997T>A|p.Ser4999Arg|14997/21291|14997/21291|4999/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1821T>A|p.Ser607Arg|1821/2796|1821/2796|607/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-976T>A|||||976|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2779T>A|||||2779|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4360T>A|||||4360|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1778T>A|||||1778|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4289T>A|||||4289|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4289T>A|||||4289|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3419T>A|||||3419|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3419T>A|||||3419|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3170T>A|||||3170|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3170T>A|||||3170|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2576T>A|||||2576|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2576T>A|||||2576|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2237T>A|||||2237|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2237T>A|||||2237|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1820T>A|||||1820|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1820T>A|||||1820|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1781T>A|||||1781|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:791:1:17:0,-4.92268,-69.8095

-NC_045512.2	15337	.	A	G	4.05319E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=7.35324;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.6766;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1501;RO=39;RPL=1;RPP=3.0103;RPPR=3.06598;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15073A>G|p.Met5025Val|15073/21291|15073/21291|5025/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1897A>G|p.Met633Val|1897/2796|1897/2796|633/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-900A>G|||||900|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2703A>G|||||2703|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4284A>G|||||4284|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1854A>G|||||1854|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4365A>G|||||4365|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4365A>G|||||4365|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3495A>G|||||3495|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3495A>G|||||3495|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3246A>G|||||3246|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3246A>G|||||3246|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2652A>G|||||2652|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2652A>G|||||2652|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2313A>G|||||2313|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2313A>G|||||2313|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1896A>G|||||1896|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1896A>G|||||1896|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1857A>G|||||1857|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:39,2:39:1501:2:77:0,-5.03309,-128.056

-NC_045512.2	15343	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.3553;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1543;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15079T>C|p.Ser5027Pro|15079/21291|15079/21291|5027/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1903T>C|p.Ser635Pro|1903/2796|1903/2796|635/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-894T>C|||||894|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2697T>C|||||2697|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4278T>C|||||4278|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1860T>C|||||1860|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4371T>C|||||4371|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4371T>C|||||4371|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3501T>C|||||3501|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3501T>C|||||3501|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3252T>C|||||3252|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3252T>C|||||3252|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2658T>C|||||2658|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2658T>C|||||2658|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2319T>C|||||2319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2319T>C|||||2319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1902T>C|||||1902|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1902T>C|||||1902|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1863T>C|||||1863|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1543:1:15:0,-10.8422,-137.641

-NC_045512.2	15376	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=81.4005;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.5855;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1491;RO=40;RPL=1;RPP=5.18177;RPPR=3.22745;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15112T>A|p.Cys5038Ser|15112/21291|15112/21291|5038/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1936T>A|p.Cys646Ser|1936/2796|1936/2796|646/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-861T>A|||||861|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2664T>A|||||2664|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4245T>A|||||4245|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1893T>A|||||1893|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4404T>A|||||4404|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4404T>A|||||4404|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3534T>A|||||3534|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3534T>A|||||3534|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3285T>A|||||3285|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3285T>A|||||3285|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2691T>A|||||2691|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2691T>A|||||2691|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2352T>A|||||2352|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2352T>A|||||2352|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1935T>A|||||1935|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1935T>A|||||1935|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1896T>A|||||1896|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1491:1:14:0,-10.9422,-133.06

-NC_045512.2	15389	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=81.4005;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.3553;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1488;RO=40;RPL=1;RPP=5.18177;RPPR=3.22745;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15125A>C|p.His5042Pro|15125/21291|15125/21291|5042/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1949A>C|p.His650Pro|1949/2796|1949/2796|650/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-848A>C|||||848|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2651A>C|||||2651|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4232A>C|||||4232|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1906A>C|||||1906|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4417A>C|||||4417|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4417A>C|||||4417|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3547A>C|||||3547|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3547A>C|||||3547|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3298A>C|||||3298|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3298A>C|||||3298|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2704A>C|||||2704|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2704A>C|||||2704|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2365A>C|||||2365|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2365A>C|||||2365|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1948A>C|||||1948|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1948A>C|||||1948|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1909A>C|||||1909|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1488:1:15:0,-10.8422,-132.699

-NC_045512.2	15413	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=81.4005;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.3553;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1530;RO=40;RPL=1;RPP=5.18177;RPPR=3.22745;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15149A>C|p.Glu5050Ala|15149/21291|15149/21291|5050/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1973A>C|p.Glu658Ala|1973/2796|1973/2796|658/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-824A>C|||||824|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2627A>C|||||2627|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4208A>C|||||4208|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1930A>C|||||1930|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4441A>C|||||4441|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4441A>C|||||4441|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3571A>C|||||3571|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3571A>C|||||3571|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3322A>C|||||3322|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3322A>C|||||3322|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2728A>C|||||2728|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2728A>C|||||2728|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2389A>C|||||2389|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2389A>C|||||2389|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1972A>C|||||1972|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1972A>C|||||1972|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1933A>C|||||1933|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1530:1:15:0,-10.8422,-136.476

-NC_045512.2	15523	.	A	G	1.31392E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.704;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1510;RO=39;RPL=0;RPP=5.18177;RPPR=3.06598;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15259A>G|p.Asn5087Asp|15259/21291|15259/21291|5087/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2083A>G|p.Asn695Asp|2083/2796|2083/2796|695/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-714A>G|||||714|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2517A>G|||||2517|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4098A>G|||||4098|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2040A>G|||||2040|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4551A>G|||||4551|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4551A>G|||||4551|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3681A>G|||||3681|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3681A>G|||||3681|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3432A>G|||||3432|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3432A>G|||||3432|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2838A>G|||||2838|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2838A>G|||||2838|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2499A>G|||||2499|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2499A>G|||||2499|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2082A>G|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2082A>G|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2043A>G|||||2043|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1510:1:38:0,-8.24393,-132.374

-NC_045512.2	15549	.	TGT	TT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=42;DPB=41.6667;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.6567;PAIRED=1;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1528;RO=41;RPL=1;RPP=5.18177;RPPR=4.33437;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=4.33437;SRR=18;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15286delG|p.Val5096fs|15286/21291|15286/21291|5096/7096||,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2110delG|p.Val704fs|2110/2796|2110/2796|704/931||WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-687delG|||||687|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2490delG|||||2490|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4071delG|||||4071|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2067delG|||||2067|,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4578delG|||||4578|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4578delG|||||4578|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3708delG|||||3708|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3708delG|||||3708|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3459delG|||||3459|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3459delG|||||3459|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2865delG|||||2865|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2865delG|||||2865|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2526delG|||||2526|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2526delG|||||2526|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2109delG|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2109delG|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2070delG|||||2070|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1528:1:37:0,-8.94543,-134.102

-NC_045512.2	15555	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4815;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1390;RO=38;RPL=0;RPP=5.18177;RPPR=5.06748;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=5.06748;SRR=16;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15291T>C|p.Asn5097Asn|15291/21291|15291/21291|5097/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2115T>C|p.Asn705Asn|2115/2796|2115/2796|705/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-682T>C|||||682|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2485T>C|||||2485|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4066T>C|||||4066|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2072T>C|||||2072|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4583T>C|||||4583|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4583T>C|||||4583|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3713T>C|||||3713|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3713T>C|||||3713|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3464T>C|||||3464|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3464T>C|||||3464|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2870T>C|||||2870|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2870T>C|||||2870|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2531T>C|||||2531|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2531T>C|||||2531|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2114T>C|||||2114|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2114T>C|||||2114|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2075T>C|||||2075|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1390:1:20:0,-9.74021,-123.383

-NC_045512.2	15556	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.0355;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1281;RO=35;RPL=0;RPP=5.18177;RPPR=8.03571;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=8.03571;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15292G>T|p.Ala5098Ser|15292/21291|15292/21291|5098/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2116G>T|p.Ala706Ser|2116/2796|2116/2796|706/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-681G>T|||||681|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2484G>T|||||2484|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4065G>T|||||4065|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2073G>T|||||2073|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4584G>T|||||4584|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4584G>T|||||4584|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3714G>T|||||3714|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3714G>T|||||3714|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3465G>T|||||3465|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3465G>T|||||3465|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2871G>T|||||2871|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2871G>T|||||2871|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2532G>T|||||2532|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2532G>T|||||2532|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2115G>T|||||2115|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2115G>T|||||2115|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2076G>T|||||2076|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1281:1:39:0,-6.94052,-111.686

-NC_045512.2	15559	.	C	T	1.08534E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.5691;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1187;RO=32;RPL=1;RPP=5.18177;RPPR=16.3106;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=23;SRP=16.3106;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15295C>T|p.Leu5099Phe|15295/21291|15295/21291|5099/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2119C>T|p.Leu707Phe|2119/2796|2119/2796|707/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-678C>T|||||678|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2481C>T|||||2481|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4062C>T|||||4062|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2076C>T|||||2076|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4587C>T|||||4587|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4587C>T|||||4587|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3717C>T|||||3717|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3717C>T|||||3717|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3468C>T|||||3468|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3468C>T|||||3468|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2874C>T|||||2874|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2874C>T|||||2874|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2535C>T|||||2535|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2535C>T|||||2535|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2118C>T|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2118C>T|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2079C>T|||||2079|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:33:32,1:32:1187:1:32:0,-6.73468,-103.927

-NC_045512.2	15683	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=46;DPB=46;DPRA=0;EPP=5.18177;EPPR=100.727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=63.6322;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1679;RO=45;RPL=1;RPP=5.18177;RPPR=3.05855;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=3.05855;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15419A>G|p.Tyr5140Cys|15419/21291|15419/21291|5140/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2243A>G|p.Tyr748Cys|2243/2796|2243/2796|748/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-554A>G|||||554|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2357A>G|||||2357|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3938A>G|||||3938|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4976A>G|||||4976|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2200A>G|||||2200|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4711A>G|||||4711|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4711A>G|||||4711|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3841A>G|||||3841|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3841A>G|||||3841|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3592A>G|||||3592|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3592A>G|||||3592|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2998A>G|||||2998|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2998A>G|||||2998|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2659A>G|||||2659|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2659A>G|||||2659|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2242A>G|||||2242|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2242A>G|||||2242|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2203A>G|||||2203|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:46:45,1:45:1679:1:13:0,-12.5474,-150.065

-NC_045512.2	15814	.	GTTTTTATG	GTTTTATG	1.40218E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D7M;DP=23;DPB=22.8889;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.4617;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=836;RO=22;RPL=1;RPP=5.18177;RPPR=50.7827;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=50.7827;SRR=22;TYPE=del;ANN=GTTTTATG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15555delT|p.Phe5185fs|15555/21291|15555/21291|5185/7096||,GTTTTATG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2379delT|p.Phe793fs|2379/2796|2379/2796|793/931||WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-418delT|||||418|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2221delT|||||2221|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3802delT|||||3802|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4840delT|||||4840|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2336delT|||||2336|,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4847delT|||||4847|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4847delT|||||4847|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3977delT|||||3977|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3977delT|||||3977|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3728delT|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3728delT|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3134delT|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3134delT|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2795delT|||||2795|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2795delT|||||2795|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2378delT|||||2378|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2378delT|||||2378|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2339delT|||||2339|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:836:1:39:0,-3.02713,-71.6684

-NC_045512.2	15829	.	G	A	3.40227E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.1128;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=1028;RO=27;RPL=0;RPP=5.18177;RPPR=32.0437;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=32.0437;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15565G>A|p.Ala5189Thr|15565/21291|15565/21291|5189/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2389G>A|p.Ala797Thr|2389/2796|2389/2796|797/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-408G>A|||||408|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2211G>A|||||2211|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3792G>A|||||3792|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4830G>A|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2346G>A|||||2346|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4857G>A|||||4857|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4857G>A|||||4857|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3987G>A|||||3987|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3987G>A|||||3987|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3738G>A|||||3738|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3738G>A|||||3738|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3144G>A|||||3144|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3144G>A|||||3144|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2805G>A|||||2805|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2805G>A|||||2805|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2388G>A|||||2388|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2388G>A|||||2388|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2349G>A|||||2349|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1028:1:35:0,-4.93021,-89.3291

-NC_045512.2	15909	.	T	C	2.39814E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3171;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=522;RO=14;RPL=0;RPP=5.18177;RPPR=33.4109;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=33.4109;SRR=0;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15645T>C|p.Gly5215Gly|15645/21291|15645/21291|5215/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2469T>C|p.Gly823Gly|2469/2796|2469/2796|823/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-328T>C|||||328|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2131T>C|||||2131|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3712T>C|||||3712|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4750T>C|||||4750|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2426T>C|||||2426|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4937T>C|||||4937|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4937T>C|||||4937|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4067T>C|||||4067|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4067T>C|||||4067|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3818T>C|||||3818|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3818T>C|||||3818|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3224T>C|||||3224|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3224T>C|||||3224|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2885T>C|||||2885|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2885T>C|||||2885|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2468T>C|||||2468|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2468T>C|||||2468|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2429T>C|||||2429|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:522:1:15:0,-3.01546,-45.8213

-NC_045512.2	15994	.	G	A	5.68589E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=7.35324;EPPR=55.4358;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.3671;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=1056;RO=28;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15730G>A|p.Gly5244Ser|15730/21291|15730/21291|5244/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2554G>A|p.Gly852Ser|2554/2796|2554/2796|852/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-243G>A|||||243|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2046G>A|||||2046|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3627G>A|||||3627|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4665G>A|||||4665|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2511G>A|||||2511|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4152G>A|||||4152|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4152G>A|||||4152|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3903G>A|||||3903|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3903G>A|||||3903|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3309G>A|||||3309|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3309G>A|||||3309|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2970G>A|||||2970|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2970G>A|||||2970|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2553G>A|||||2553|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2553G>A|||||2553|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2514G>A|||||2514|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:28,2:28:1056:2:71:0,-2.28884,-88.5965

-NC_045512.2	15999	.	A	T	1.4759E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.1881;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1110;RO=29;RPL=0;RPP=5.18177;RPPR=3.08518;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15735A>T|p.Thr5245Thr|15735/21291|15735/21291|5245/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2559A>T|p.Thr853Thr|2559/2796|2559/2796|853/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-238A>T|||||238|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2041A>T|||||2041|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3622A>T|||||3622|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4660A>T|||||4660|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2516A>T|||||2516|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4157A>T|||||4157|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4157A>T|||||4157|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3908A>T|||||3908|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3908A>T|||||3908|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3314A>T|||||3314|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3314A>T|||||3314|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2975A>T|||||2975|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2975A>T|||||2975|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2558A>T|||||2558|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2558A>T|||||2558|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2519A>T|||||2519|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1110:1:16:0,-7.43092,-98.6022

-NC_045512.2	16000	.	CTTATG	CTATG	8.22728E-4	.	AB=0.133333;ABP=38.0434;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1M1D4M;DP=30;DPB=29.3333;DPRA=0;EPP=11.6962;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.57134;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=151;QR=998;RO=26;RPL=2;RPP=3.0103;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=13;SRP=3.0103;SRR=13;TYPE=del;ANN=CTATG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15738delT|p.Met5247fs|15738/21291|15738/21291|5246/7096||,CTATG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2562delT|p.Met855fs|2562/2796|2562/2796|854/931||WARNING_TRANSCRIPT_NO_START_CODON,CTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-235delT|||||235|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2038delT|||||2038|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3619delT|||||3619|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4657delT|||||4657|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2519delT|||||2519|,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4160delT|||||4160|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4160delT|||||4160|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3911delT|||||3911|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3911delT|||||3911|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3317delT|||||3317|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3317delT|||||3317|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2978delT|||||2978|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2978delT|||||2978|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2561delT|||||2561|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2561delT|||||2561|WARNING_TRANSCRIPT_NO_START_CODON,CTATG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2522delT|||||2522|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:30:26,4:26:998:4:151:-4.92664,0,-81.0997

-NC_045512.2	16257	.	T	G	1.63712E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7911;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=348;RO=9;RPL=0;RPP=5.18177;RPPR=9.04217;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15993T>G|p.Leu5331Leu|15993/21291|15993/21291|5331/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.21T>G|p.Leu7Leu|21/1803|21/1803|7/600||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1783T>G|||||1783|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3364T>G|||||3364|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4402T>G|||||4402|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2774T>G|||||2774|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4415T>G|||||4415|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4415T>G|||||4415|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4166T>G|||||4166|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4166T>G|||||4166|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3572T>G|||||3572|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3572T>G|||||3572|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3233T>G|||||3233|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3233T>G|||||3233|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2816T>G|||||2816|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2816T>G|||||2816|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2777T>G|||||2777|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*21T>G|||||21|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:348:1:15:0,-1.51031,-30.1801

-NC_045512.2	16394	.	C	T	0.0115511	.	AB=0.142857;ABP=10.7656;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.9282;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=233;RO=6;RPL=1;RPP=5.18177;RPPR=16.0391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=16.0391;SRR=6;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16130C>T|p.Pro5377Leu|16130/21291|16130/21291|5377/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.158C>T|p.Pro53Leu|158/1803|158/1803|53/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1646C>T|||||1646|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3227C>T|||||3227|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4265C>T|||||4265|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2911C>T|||||2911|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4552C>T|||||4552|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4552C>T|||||4552|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4303C>T|||||4303|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4303C>T|||||4303|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3709C>T|||||3709|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3709C>T|||||3709|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3370C>T|||||3370|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3370C>T|||||3370|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2953C>T|||||2953|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2953C>T|||||2953|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2914C>T|||||2914|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*158C>T|||||158|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:6,1:6:233:1:37:-1.59062,0,-19.2329

-NC_045512.2	16410	.	A	C	9.23317E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.7587;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=234;RO=6;RPL=1;RPP=5.18177;RPPR=16.0391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=16.0391;SRR=6;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16146A>C|p.Thr5382Thr|16146/21291|16146/21291|5382/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.174A>C|p.Thr58Thr|174/1803|174/1803|58/600||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1630A>C|||||1630|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3211A>C|||||3211|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4249A>C|||||4249|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2927A>C|||||2927|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4568A>C|||||4568|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4568A>C|||||4568|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4319A>C|||||4319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4319A>C|||||4319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3725A>C|||||3725|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3725A>C|||||3725|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3386A>C|||||3386|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3386A>C|||||3386|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2969A>C|||||2969|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2969A>C|||||2969|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2930A>C|||||2930|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*174A>C|||||174|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:7:6,1:6:234:1:16:0,-0.507227,-19.8311

-NC_045512.2	16418	.	C	A	1.29718E-4	.	AB=0.1;ABP=16.9077;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.4187;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=313;RO=9;RPL=0;RPP=5.18177;RPPR=9.04217;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=9.04217;SRR=7;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16154C>A|p.Thr5385Asn|16154/21291|16154/21291|5385/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.182C>A|p.Thr61Asn|182/1803|182/1803|61/600||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1622C>A|||||1622|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3203C>A|||||3203|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4241C>A|||||4241|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2935C>A|||||2935|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4576C>A|||||4576|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4576C>A|||||4576|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4327C>A|||||4327|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4327C>A|||||4327|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3733C>A|||||3733|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3733C>A|||||3733|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3394C>A|||||3394|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3394C>A|||||3394|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2977C>A|||||2977|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2977C>A|||||2977|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2938C>A|||||2938|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*182C>A|||||182|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:9,1:9:313:1:34:-0.388611,0,-25.4891

-NC_045512.2	16488	.	TGC	TC	3.07862E-5	.	AB=0.111111;ABP=26.6552;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M1D1M;DP=18;DPB=17.3333;DPRA=0;EPP=7.35324;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.857;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=611;RO=16;RPL=0;RPP=7.35324;RPPR=3.55317;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=9;SRP=3.55317;SRR=7;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16225delG|p.Ala5409fs|16225/21291|16225/21291|5409/7096||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.253delG|p.Ala85fs|253/1803|253/1803|85/600||WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1551delG|||||1551|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3132delG|||||3132|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4170delG|||||4170|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3006delG|||||3006|,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4647delG|||||4647|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4647delG|||||4647|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4398delG|||||4398|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4398delG|||||4398|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3804delG|||||3804|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3804delG|||||3804|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3465delG|||||3465|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3465delG|||||3465|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3048delG|||||3048|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3048delG|||||3048|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3009delG|||||3009|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*253delG|||||253|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:18:16,2:16:611:2:77:-1.8906,0,-49.9112

-NC_045512.2	16751	.	CTA	CA	1.06969E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=17;DPB=16.6667;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.8219;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=589;RO=16;RPL=0;RPP=5.18177;RPPR=7.89611;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=7.89611;SRR=11;TYPE=del;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16488delT|p.Arg5497fs|16488/21291|16488/21291|5496/7096||,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.516delT|p.Arg173fs|516/1803|516/1803|172/600||WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4811delT|||||4811|,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1288delT|||||1288|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2869delT|||||2869|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3907delT|||||3907|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3269delT|||||3269|,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4910delT|||||4910|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4910delT|||||4910|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4661delT|||||4661|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4661delT|||||4661|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4067delT|||||4067|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4067delT|||||4067|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3728delT|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3728delT|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3311delT|||||3311|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3311delT|||||3311|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3272delT|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,CA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*516delT|||||516|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:589:1:33:0,-1.81837,-50.0431

-NC_045512.2	16767	.	C	T	1.29273E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.2377;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=753;RO=20;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16503C>T|p.Asn5501Asn|16503/21291|16503/21291|5501/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.531C>T|p.Asn177Asn|531/1803|531/1803|177/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4796C>T|||||4796|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1273C>T|||||1273|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2854C>T|||||2854|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3892C>T|||||3892|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3284C>T|||||3284|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4925C>T|||||4925|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4925C>T|||||4925|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4676C>T|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4676C>T|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4082C>T|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4082C>T|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3743C>T|||||3743|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3743C>T|||||3743|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3326C>T|||||3326|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3326C>T|||||3326|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3287C>T|||||3287|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*531C>T|||||531|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:753:1:37:0,-2.6238,-64.4021

-NC_045512.2	16867	.	T	C	4.11207E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.8701;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=351;RO=9;RPL=0;RPP=5.18177;RPPR=22.5536;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=22.5536;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16603T>C|p.Tyr5535His|16603/21291|16603/21291|5535/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.631T>C|p.Tyr211His|631/1803|631/1803|211/600||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4696T>C|||||4696|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1173T>C|||||1173|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2754T>C|||||2754|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3792T>C|||||3792|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3384T>C|||||3384|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4776T>C|||||4776|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4776T>C|||||4776|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4182T>C|||||4182|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4182T>C|||||4182|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3843T>C|||||3843|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3843T>C|||||3843|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3426T>C|||||3426|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3426T>C|||||3426|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3387T>C|||||3387|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*631T>C|||||631|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:351:1:19:0,-1.11033,-30.0519

-NC_045512.2	17067	.	T	A	2.83155E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.151;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=623;RO=17;RPL=0;RPP=5.18177;RPPR=4.1599;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=4.1599;SRR=10;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16803T>A|p.Tyr5601*|16803/21291|16803/21291|5601/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.831T>A|p.Tyr277*|831/1803|831/1803|277/600||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4496T>A|||||4496|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-973T>A|||||973|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2554T>A|||||2554|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3592T>A|||||3592|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3584T>A|||||3584|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4976T>A|||||4976|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4976T>A|||||4976|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4382T>A|||||4382|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4382T>A|||||4382|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4043T>A|||||4043|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4043T>A|||||4043|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3626T>A|||||3626|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3626T>A|||||3626|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3587T>A|||||3587|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*831T>A|||||831|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:623:1:33:0,-2.1194,-53.1015

-NC_045512.2	17077	.	C	T	1.31241E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.439;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=896;RO=24;RPL=0;RPP=5.18177;RPPR=4.45795;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=4.45795;SRR=10;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16813C>T|p.Gln5605*|16813/21291|16813/21291|5605/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.841C>T|p.Gln281*|841/1803|841/1803|281/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4486C>T|||||4486|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-963C>T|||||963|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2544C>T|||||2544|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3582C>T|||||3582|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3594C>T|||||3594|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4986C>T|||||4986|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4986C>T|||||4986|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4392C>T|||||4392|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4392C>T|||||4392|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4053C>T|||||4053|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4053C>T|||||4053|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3636C>T|||||3636|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3636C>T|||||3636|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3597C>T|||||3597|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*841C>T|||||841|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:896:1:16:0,-5.92577,-79.36

-NC_045512.2	17126	.	TCTACTAC	TCTAC	9.60056E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M3D4M;DP=25;DPB=24.625;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.1509;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=908;RO=24;RPL=0;RPP=5.18177;RPPR=4.45795;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=4.45795;SRR=10;TYPE=del;ANN=TCTAC|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16867_16869delTAC|p.Tyr5623del|16867/21291|16867/21291|5623/7096||,TCTAC|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.895_897delTAC|p.Tyr299del|895/1803|895/1803|299/600||WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4432_-4430delTAC|||||4432|,TCTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-909_-907delTAC|||||909|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2490_-2488delTAC|||||2490|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3528_-3526delTAC|||||3528|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3648_*3650delTAC|||||3648|,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4446_*4448delTAC|||||4446|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4446_*4448delTAC|||||4446|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4107_*4109delTAC|||||4107|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4107_*4109delTAC|||||4107|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3690_*3692delTAC|||||3690|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3690_*3692delTAC|||||3690|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3651_*3653delTAC|||||3651|WARNING_TRANSCRIPT_NO_START_CODON,TCTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*895_*897delTAC|||||895|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:908:1:39:0,-3.62919,-78.1424

-NC_045512.2	17139	.	TGC	TC	2.41873E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=25;DPB=24.6667;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.5266;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=890;RO=24;RPL=1;RPP=5.18177;RPPR=6.26751;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=6.26751;SRR=9;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16876delG|p.Ala5626fs|16876/21291|16876/21291|5626/7096||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.904delG|p.Ala302fs|904/1803|904/1803|302/600||WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4423delG|||||4423|,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-900delG|||||900|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2481delG|||||2481|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3519delG|||||3519|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3657delG|||||3657|,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4455delG|||||4455|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4455delG|||||4455|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4116delG|||||4116|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4116delG|||||4116|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3699delG|||||3699|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3699delG|||||3699|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3660delG|||||3660|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*904delG|||||904|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:890:1:33:0,-4.22661,-77.1178

-NC_045512.2	17168	.	A	T	3.01908E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.0869;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=545;RO=14;RPL=0;RPP=5.18177;RPPR=33.4109;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=33.4109;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16904A>T|p.His5635Leu|16904/21291|16904/21291|5635/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.932A>T|p.His311Leu|932/1803|932/1803|311/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4395A>T|||||4395|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-872A>T|||||872|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2453A>T|||||2453|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3491A>T|||||3491|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3685A>T|||||3685|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4483A>T|||||4483|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4483A>T|||||4483|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4144A>T|||||4144|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4144A>T|||||4144|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3727A>T|||||3727|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3727A>T|||||3727|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3688A>T|||||3688|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*932A>T|||||932|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:545:1:16:0,-2.91547,-47.7963

-NC_045512.2	17196	.	G	T	8.97212E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=13.3567;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.6029;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=630;RO=17;RPL=1;RPP=5.18177;RPPR=4.1599;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=18.4661;SRR=3;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16932G>T|p.Lys5644Asn|16932/21291|16932/21291|5644/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.960G>T|p.Lys320Asn|960/1803|960/1803|320/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4367G>T|||||4367|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-844G>T|||||844|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2425G>T|||||2425|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3463G>T|||||3463|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3713G>T|||||3713|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4511G>T|||||4511|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4511G>T|||||4511|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4172G>T|||||4172|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4172G>T|||||4172|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3755G>T|||||3755|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3755G>T|||||3755|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3716G>T|||||3716|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*960G>T|||||960|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:630:1:18:0,-3.61857,-55.2255

-NC_045512.2	17203	.	A	G	1.80063E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.5869;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1109;RO=29;RPL=1;RPP=5.18177;RPPR=3.08518;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=3.08518;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16939A>G|p.Lys5647Glu|16939/21291|16939/21291|5647/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.967A>G|p.Lys323Glu|967/1803|967/1803|323/600||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4360A>G|||||4360|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-837A>G|||||837|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2418A>G|||||2418|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3456A>G|||||3456|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3720A>G|||||3720|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4518A>G|||||4518|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4518A>G|||||4518|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4179A>G|||||4179|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4179A>G|||||4179|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3762A>G|||||3762|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3762A>G|||||3762|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3723A>G|||||3723|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*967A>G|||||967|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1109:1:36:0,-5.43262,-96.5173

-NC_045512.2	17213	.	C	T	8.13698E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.6558;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1119;RO=29;RPL=0;RPP=5.18177;RPPR=3.08518;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16949C>T|p.Pro5650Leu|16949/21291|16949/21291|5650/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.977C>T|p.Pro326Leu|977/1803|977/1803|326/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4350C>T|||||4350|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-827C>T|||||827|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2408C>T|||||2408|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3446C>T|||||3446|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3730C>T|||||3730|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4528C>T|||||4528|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4528C>T|||||4528|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4189C>T|||||4189|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4189C>T|||||4189|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3772C>T|||||3772|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3772C>T|||||3772|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3733C>T|||||3733|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*977C>T|||||977|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1119:1:27:0,-6.33112,-98.3122

-NC_045512.2	17259	.	G	T	0.00155336	.	AB=0.133333;ABP=38.0434;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=11.6962;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.93571;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=154;QR=1000;RO=26;RPL=2;RPP=3.0103;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16995G>T|p.Glu5665Asp|16995/21291|16995/21291|5665/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1023G>T|p.Glu341Asp|1023/1803|1023/1803|341/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4304G>T|||||4304|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-781G>T|||||781|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2362G>T|||||2362|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3400G>T|||||3400|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3776G>T|||||3776|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4574G>T|||||4574|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4574G>T|||||4574|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4235G>T|||||4235|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4235G>T|||||4235|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3818G>T|||||3818|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3818G>T|||||3818|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3779G>T|||||3779|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1023G>T|||||1023|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:30:26,4:26:1000:4:154:-5.20269,0,-81.2789

-NC_045512.2	17410	.	C	T	6.91305E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=7.35324;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.5212;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=1222;RO=32;RPL=0;RPP=7.35324;RPPR=3.28173;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=3.28173;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17146C>T|p.Arg5716Cys|17146/21291|17146/21291|5716/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1174C>T|p.Arg392Cys|1174/1803|1174/1803|392/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4153C>T|||||4153|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-630C>T|||||630|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2211C>T|||||2211|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3249C>T|||||3249|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3927C>T|||||3927|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4725C>T|||||4725|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4725C>T|||||4725|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4386C>T|||||4386|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4386C>T|||||4386|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3969C>T|||||3969|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3969C>T|||||3969|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3930C>T|||||3930|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1174C>T|||||1174|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:32,2:32:1222:2:78:0,-2.83155,-102.874

-NC_045512.2	17446	.	C	A	2.51182E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.8591;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1131;RO=30;RPL=1;RPP=5.18177;RPPR=7.64277;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=7.64277;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17182C>A|p.Gln5728Lys|17182/21291|17182/21291|5728/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1210C>A|p.Gln404Lys|1210/1803|1210/1803|404/600||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4117C>A|||||4117|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-594C>A|||||594|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2175C>A|||||2175|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3213C>A|||||3213|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3963C>A|||||3963|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4761C>A|||||4761|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4761C>A|||||4761|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4422C>A|||||4422|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4422C>A|||||4422|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4005C>A|||||4005|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4005C>A|||||4005|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3966C>A|||||3966|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1210C>A|||||1210|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1131:1:32:0,-6.13262,-98.892

-NC_045512.2	17569	.	CCTGCTGA	CCTGA	68.1387	.	AB=0.210526;ABP=30.668;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1M3D4M;DP=38;DPB=35;DPRA=0;EPP=20.3821;EPPR=68.1545;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.6895;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=302;QR=1163;RO=30;RPL=4;RPP=3.0103;RPPR=3.0103;RPR=4;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=15;SRP=3.0103;SRR=15;TYPE=del;ANN=CCTGA|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17309_17311delCTG|p.Ala5770del|17309/21291|17309/21291|5770/7096||,CCTGA|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1337_1339delCTG|p.Ala446del|1337/1803|1337/1803|446/600||WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3990_-3988delCTG|||||3990|,CCTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-467_-465delCTG|||||467|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2048_-2046delCTG|||||2048|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3086_-3084delCTG|||||3086|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4090_*4092delCTG|||||4090|,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4888_*4890delCTG|||||4888|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4888_*4890delCTG|||||4888|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4549_*4551delCTG|||||4549|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4549_*4551delCTG|||||4549|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4132_*4134delCTG|||||4132|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4132_*4134delCTG|||||4132|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4093_*4095delCTG|||||4093|WARNING_TRANSCRIPT_NO_START_CODON,CCTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1337_*1339delCTG|||||1337|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:38:30,8:30:1163:8:302:-16.0982,0,-93.5299

-NC_045512.2	17658	.	GTTTTATAAG	GTTTATAAG	2.95717E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D8M;DP=19;DPB=18.9;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.1076;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=684;RO=18;RPL=1;RPP=5.18177;RPPR=42.0968;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=42.0968;SRR=18;TYPE=del;ANN=GTTTATAAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17398delT|p.Tyr5800fs|17398/21291|17398/21291|5800/7096||,GTTTATAAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1426delT|p.Tyr476fs|1426/1803|1426/1803|476/600||WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3901delT|||||3901|,GTTTATAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-378delT|||||378|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1959delT|||||1959|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2997delT|||||2997|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4179delT|||||4179|,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4977delT|||||4977|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4977delT|||||4977|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4638delT|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4638delT|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4221delT|||||4221|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4221delT|||||4221|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4182delT|||||4182|WARNING_TRANSCRIPT_NO_START_CODON,GTTTATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1426delT|||||1426|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:684:1:39:0,-1.82301,-57.9989

-NC_045512.2	17760	.	A	G	1.69337E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.3625;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=560;RO=16;RPL=1;RPP=5.18177;RPPR=11.6962;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=11.6962;SRR=12;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17496A>G|p.Lys5832Lys|17496/21291|17496/21291|5832/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1524A>G|p.Lys508Lys|1524/1803|1524/1803|508/600||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3803A>G|||||3803|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-280A>G|||||280|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1861A>G|||||1861|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2899A>G|||||2899|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4277A>G|||||4277|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4736A>G|||||4736|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4736A>G|||||4736|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4319A>G|||||4319|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4319A>G|||||4319|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4280A>G|||||4280|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1524A>G|||||1524|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:560:1:35:0,-1.61888,-47.2278

-NC_045512.2	17968	.	G	T	2.63493E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.3152;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=421;RO=12;RPL=0;RPP=5.18177;RPPR=5.9056;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=5.9056;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17704G>T|p.Asp5902Tyr|17704/21291|17704/21291|5902/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1732G>T|p.Asp578Tyr|1732/1803|1732/1803|578/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3595G>T|||||3595|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-72G>T|||||72|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1653G>T|||||1653|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2691G>T|||||2691|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4485G>T|||||4485|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4944G>T|||||4944|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4944G>T|||||4944|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4527G>T|||||4527|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4527G>T|||||4527|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4488G>T|||||4488|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1732G>T|||||1732|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:421:1:34:0,-0.514479,-34.8226

-NC_045512.2	17995	.	T	C	7.64275E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.3796;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=908;RO=24;RPL=0;RPP=5.18177;RPPR=26.1727;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=26.1727;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17731T>C|p.Phe5911Leu|17731/21291|17731/21291|5911/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1759T>C|p.Phe587Leu|1759/1803|1759/1803|587/600||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3568T>C|||||3568|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-45T>C|||||45|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1626T>C|||||1626|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2664T>C|||||2664|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4512T>C|||||4512|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4971T>C|||||4971|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4971T>C|||||4971|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4554T>C|||||4554|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4554T>C|||||4554|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4515T>C|||||4515|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1759T>C|||||1759|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:908:1:38:0,-3.72848,-78.2334

-NC_045512.2	18059	.	T	A	9.44634E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.1509;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=916;RO=24;RPL=0;RPP=5.18177;RPPR=32.3252;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=32.3252;SRR=3;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17795T>A|p.Leu5932His|17795/21291|17795/21291|5932/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.20T>A|p.Leu7His|20/1581|20/1581|7/526||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3504T>A|||||3504|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1562T>A|||||1562|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2600T>A|||||2600|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4576T>A|||||4576|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4618T>A|||||4618|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4618T>A|||||4618|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4579T>A|||||4579|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1823T>A|||||1823|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*20T>A|||||20|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:916:1:39:0,-3.62919,-78.8594

-NC_045512.2	18109	.	C	T	2.73524E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=43;DPB=43;DPRA=0;EPP=5.18177;EPPR=77.6676;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.0802;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1617;RO=42;RPL=0;RPP=5.18177;RPPR=3.21711;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.21711;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17845C>T|p.Pro5949Ser|17845/21291|17845/21291|5949/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.70C>T|p.Pro24Ser|70/1581|70/1581|24/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3454C>T|||||3454|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1512C>T|||||1512|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2550C>T|||||2550|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4626C>T|||||4626|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4668C>T|||||4668|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4668C>T|||||4668|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4629C>T|||||4629|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1873C>T|||||1873|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*70C>T|||||70|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:43:42,1:42:1617:1:15:0,-11.4443,-144.298

-NC_045512.2	18215	.	GTTTTAAAA	GTTTAAAA	7.19933E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D7M;DP=27;DPB=26.8889;DPRA=0;EPP=5.18177;EPPR=36.4176;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.8466;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=997;RO=26;RPL=0;RPP=5.18177;RPPR=8.35546;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=19.3799;SRR=20;TYPE=del;ANN=GTTTAAAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17955delT|p.Phe5985fs|17955/21291|17955/21291|5985/7096||,GTTTAAAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.180delT|p.Phe60fs|180/1581|180/1581|60/526||WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3344delT|||||3344|,GTTTAAAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1402delT|||||1402|WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2440delT|||||2440|WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4736delT|||||4736|,GTTTAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4778delT|||||4778|WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4778delT|||||4778|WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4739delT|||||4739|WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1983delT|||||1983|WARNING_TRANSCRIPT_NO_START_CODON,GTTTAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*180delT|||||180|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:997:1:39:0,-4.23125,-86.1467

-NC_045512.2	18345	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.7841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1204;RO=35;RPL=0;RPP=5.18177;RPPR=3.07234;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18081T>G|p.Gly6027Gly|18081/21291|18081/21291|6027/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.306T>G|p.Gly102Gly|306/1581|306/1581|102/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3218T>G|||||3218|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1276T>G|||||1276|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2314T>G|||||2314|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4862T>G|||||4862|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4904T>G|||||4904|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4904T>G|||||4904|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4865T>G|||||4865|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2109T>G|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*306T>G|||||306|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1204:1:14:0,-9.43709,-107.255

-NC_045512.2	18346	.	A	C	1.46161E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.8233;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1207;RO=34;RPL=1;RPP=5.18177;RPPR=3.26577;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18082A>C|p.Thr6028Pro|18082/21291|18082/21291|6028/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.307A>C|p.Thr103Pro|307/1581|307/1581|103/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3217A>C|||||3217|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1275A>C|||||1275|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2313A>C|||||2313|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4863A>C|||||4863|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4905A>C|||||4905|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4905A>C|||||4905|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4866A>C|||||4866|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2110A>C|||||2110|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*307A>C|||||307|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:34,1:34:1207:1:34:0,-7.13714,-105.526

-NC_045512.2	18368	.	G	T	1.1206E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.7754;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=654;RO=17;RPL=0;RPP=5.18177;RPPR=39.9253;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=39.9253;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18104G>T|p.Gly6035Val|18104/21291|18104/21291|6035/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.329G>T|p.Gly110Val|329/1581|329/1581|110/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3195G>T|||||3195|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1253G>T|||||1253|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2291G>T|||||2291|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4885G>T|||||4885|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4927G>T|||||4927|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4927G>T|||||4927|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4888G>T|||||4888|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2132G>T|||||2132|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*329G>T|||||329|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:654:1:39:0,-1.52198,-55.3003

-NC_045512.2	18427	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.4112;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1324;RO=35;RPL=0;RPP=5.18177;RPPR=3.07234;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18163A>C|p.Asn6055His|18163/21291|18163/21291|6055/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.388A>C|p.Asn130His|388/1581|388/1581|130/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3136A>C|||||3136|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1194A>C|||||1194|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2232A>C|||||2232|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4944A>C|||||4944|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4986A>C|||||4986|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4986A>C|||||4986|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4947A>C|||||4947|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2191A>C|||||2191|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*388A>C|||||388|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1324:1:33:0,-7.53794,-116.149

-NC_045512.2	18482	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.7841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=1269;RO=35;RPL=0;RPP=5.18177;RPPR=3.07234;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18218A>C|p.His6073Pro|18218/21291|18218/21291|6073/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.443A>C|p.His148Pro|443/1581|443/1581|148/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3081A>C|||||3081|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1139A>C|||||1139|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2177A>C|||||2177|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4999A>C|||||4999|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2246A>C|||||2246|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*443A>C|||||443|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1269:1:14:0,-9.43709,-113.1

-NC_045512.2	18494	.	T	C	2.34758E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.0087;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1301;RO=34;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18230T>C|p.Leu6077Pro|18230/21291|18230/21291|6077/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.455T>C|p.Leu152Pro|455/1581|455/1581|152/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3069T>C|||||3069|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1127T>C|||||1127|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2165T>C|||||2165|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2258T>C|||||2258|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*455T>C|||||455|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,2:34:1301:2:77:0,-3.52794,-110.074

-NC_045512.2	18598	.	G	A	3.1823E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1059;RO=30;RPL=0;RPP=5.18177;RPPR=5.61607;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18334G>A|p.Ala6112Thr|18334/21291|18334/21291|6112/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.559G>A|p.Ala187Thr|559/1581|559/1581|187/526||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2965G>A|||||2965|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1023G>A|||||1023|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2061G>A|||||2061|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2362G>A|||||2362|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*559G>A|||||559|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1059:1:34:0,-5.93302,-92.2049

-NC_045512.2	18606	.	CTTTGA	CTTGA,CTTTGT	1.44696E-15	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D4M,5M1X;DP=37;DPB=36.8333;DPRA=0,0;EPP=5.18177,5.18177;EPPR=79.0118;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=45.1261;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=37,18;QR=1312;RO=35;RPL=0,0;RPP=5.18177,5.18177;RPPR=3.07234;RPR=1,1;RUN=1,1;SAF=1,1;SAP=5.18177,5.18177;SAR=0,0;SRF=17;SRP=3.07234;SRR=18;TYPE=del,snp;ANN=CTTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18345delT|p.Phe6115fs|18345/21291|18345/21291|6115/7096||,CTTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.570delT|p.Phe190fs|570/1581|570/1581|190/526||WARNING_TRANSCRIPT_NO_START_CODON,CTTTGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18347A>T|p.Glu6116Val|18347/21291|18347/21291|6116/7096||,CTTTGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.572A>T|p.Glu191Val|572/1581|572/1581|191/526||WARNING_TRANSCRIPT_NO_START_CODON,CTTGA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2954delT|||||2954|,CTTTGT|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2952A>T|||||2952|,CTTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1012delT|||||1012|WARNING_TRANSCRIPT_NO_START_CODON,CTTTGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1010A>T|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2050delT|||||2050|WARNING_TRANSCRIPT_NO_START_CODON,CTTTGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2048A>T|||||2048|WARNING_TRANSCRIPT_NO_START_CODON,CTTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2373delT|||||2373|WARNING_TRANSCRIPT_NO_START_CODON,CTTTGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2375A>T|||||2375|WARNING_TRANSCRIPT_NO_START_CODON,CTTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*570delT|||||570|WARNING_TRANSCRIPT_NO_START_CODON,CTTTGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*572A>T|||||572|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:35,1,1:35:1312:1,1:37,18:0,-7.41414,-114.766,-9.312,-113.753,-116.479

-NC_045512.2	18622	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.3944;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1389;RO=36;RPL=1;RPP=5.18177;RPPR=3.25157;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18358A>G|p.Met6120Val|18358/21291|18358/21291|6120/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.583A>G|p.Met195Val|583/1581|583/1581|195/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2941A>G|||||2941|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-999A>G|||||999|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2037A>G|||||2037|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2386A>G|||||2386|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*583A>G|||||583|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1389:1:39:0,-7.24155,-121.396

-NC_045512.2	18662	.	GTCTA	GCTA,GTCA	2.26918E-14	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D3M,3M1D1M;DP=34;DPB=33.6;DPRA=0,0;EPP=5.18177,5.18177;EPPR=72.4974;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=41.2727;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=37,37;QR=1176;RO=32;RPL=1,1;RPP=5.18177,5.18177;RPPR=5.45321;RPR=0,0;RUN=1,1;SAF=0,0;SAP=5.18177,5.18177;SAR=1,1;SRF=19;SRP=5.45321;SRR=13;TYPE=del,del;ANN=GCTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18399delT|p.Leu6134fs|18399/21291|18399/21291|6133/7096||,GTCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18401delT|p.Leu6134fs|18401/21291|18401/21291|6134/7096||,GCTA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.624delT|p.Leu209fs|624/1581|624/1581|208/526||WARNING_TRANSCRIPT_NO_START_CODON,GTCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.626delT|p.Leu209fs|626/1581|626/1581|209/526||WARNING_TRANSCRIPT_NO_START_CODON,GCTA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2900delT|||||2900|,GTCA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2898delT|||||2898|,GCTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-958delT|||||958|WARNING_TRANSCRIPT_NO_START_CODON,GTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-956delT|||||956|WARNING_TRANSCRIPT_NO_START_CODON,GCTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1996delT|||||1996|WARNING_TRANSCRIPT_NO_START_CODON,GTCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1994delT|||||1994|WARNING_TRANSCRIPT_NO_START_CODON,GCTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2427delT|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,GTCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2429delT|||||2429|WARNING_TRANSCRIPT_NO_START_CODON,GCTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*624delT|||||624|WARNING_TRANSCRIPT_NO_START_CODON,GTCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*626delT|||||626|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:32,1,1:32:1176:1,1:37,37:0,-6.60594,-102.439,-6.60594,-99.7133,-102.439

-NC_045512.2	18680	.	CCAC	CC	2.35278E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M2D1M;DP=19;DPB=18.5;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3362;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=669;RO=18;RPL=0;RPP=5.18177;RPPR=42.0968;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=42.0968;SRR=0;TYPE=del;ANN=CC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18419_18420delCA|p.Thr6140fs|18419/21291|18419/21291|6140/7096||INFO_REALIGN_3_PRIME,CC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.644_645delCA|p.Thr215fs|644/1581|644/1581|215/526||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CC|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2881_-2880delAC|||||2881|,CC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-939_-938delAC|||||939|WARNING_TRANSCRIPT_NO_START_CODON,CC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1977_-1976delAC|||||1977|WARNING_TRANSCRIPT_NO_START_CODON,CC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2446_*2447delAC|||||2446|WARNING_TRANSCRIPT_NO_START_CODON,CC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*643_*644delAC|||||643|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:669:1:38:0,-1.9223,-56.7357

-NC_045512.2	18730	.	A	G	6.31357E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.9827;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1421;RO=37;RPL=1;RPP=5.18177;RPPR=3.06899;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18466A>G|p.Ile6156Val|18466/21291|18466/21291|6156/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.691A>G|p.Ile231Val|691/1581|691/1581|231/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2833A>G|||||2833|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-891A>G|||||891|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1929A>G|||||1929|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2494A>G|||||2494|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*691A>G|||||691|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1421:1:38:0,-7.64187,-124.374

-NC_045512.2	18807	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.2724;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1429;RO=37;RPL=1;RPP=5.18177;RPPR=3.06899;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18543C>T|p.Asn6181Asn|18543/21291|18543/21291|6181/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.768C>T|p.Asn256Asn|768/1581|768/1581|256/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2756C>T|||||2756|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-814C>T|||||814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1852C>T|||||1852|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2571C>T|||||2571|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*768C>T|||||768|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1429:1:15:0,-9.93915,-127.39

-NC_045512.2	18907	.	GTTGA	GTGA	1.02766E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=34;DPB=33.8;DPRA=0;EPP=5.18177;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.6957;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1229;RO=33;RPL=0;RPP=5.18177;RPPR=4.65535;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=4.65535;SRR=19;TYPE=del;ANN=GTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18645delT|p.Asp6216fs|18645/21291|18645/21291|6215/7096||,GTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.870delT|p.Asp291fs|870/1581|870/1581|290/526||WARNING_TRANSCRIPT_NO_START_CODON,GTGA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2654delT|||||2654|,GTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-712delT|||||712|WARNING_TRANSCRIPT_NO_START_CODON,GTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1750delT|||||1750|WARNING_TRANSCRIPT_NO_START_CODON,GTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2673delT|||||2673|WARNING_TRANSCRIPT_NO_START_CODON,GTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*870delT|||||870|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:33,1:33:1229:1:33:0,-6.93588,-107.61

-NC_045512.2	18917	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=5.18177;EPPR=74.6689;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.7777;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1268;RO=33;RPL=0;RPP=5.18177;RPPR=4.65535;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=4.65535;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18653C>T|p.Thr6218Ile|18653/21291|18653/21291|6218/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.878C>T|p.Thr293Ile|878/1581|878/1581|293/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2646C>T|||||2646|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-704C>T|||||704|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1742C>T|||||1742|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2681C>T|||||2681|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*878C>T|||||878|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:33,1:33:1268:1:37:0,-6.53719,-110.714

-NC_045512.2	18960	.	G	A	1.67705E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=5.18177;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.4213;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1211;RO=32;RPL=1;RPP=5.18177;RPPR=3.28173;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.28173;SRR=17;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18696G>A|p.Ala6232Ala|18696/21291|18696/21291|6232/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.921G>A|p.Ala307Ala|921/1581|921/1581|307/526||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2603G>A|||||2603|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-661G>A|||||661|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1699G>A|||||1699|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2724G>A|||||2724|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*921G>A|||||921|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:33:32,1:32:1211:1:37:0,-6.23616,-105.593

-NC_045512.2	18978	.	A	C	3.04501E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=46.8017;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2968;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=891;RO=24;RPL=1;RPP=5.18177;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=6.26751;SRR=9;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18714A>C|p.Gln6238His|18714/21291|18714/21291|6238/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.939A>C|p.Gln313His|939/1581|939/1581|313/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2585A>C|||||2585|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-643A>C|||||643|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1681A>C|||||1681|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2742A>C|||||2742|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*939A>C|||||939|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:891:1:34:0,-4.12684,-77.1064

-NC_045512.2	18984	.	G	T	4.03517E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.0994;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=584;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=35.5824;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18720G>T|p.Met6240Ile|18720/21291|18720/21291|6240/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.945G>T|p.Met315Ile|945/1581|945/1581|315/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2579G>T|||||2579|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-637G>T|||||637|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1675G>T|||||1675|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2748G>T|||||2748|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*945G>T|||||945|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:584:1:13:0,-3.51649,-51.6033

-NC_045512.2	18996	.	T	C	1.59375E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=27.4756;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1206;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=581;RO=15;RPL=0;RPP=5.18177;RPPR=35.5824;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=27.4756;SRR=1;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18732T>C|p.Ala6244Ala|18732/21291|18732/21291|6244/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.957T>C|p.Ala319Ala|957/1581|957/1581|319/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2567T>C|||||2567|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-625T>C|||||625|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1663T>C|||||1663|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2760T>C|||||2760|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*957T>C|||||957|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:581:1:39:0,-0.919915,-48.7365

-NC_045512.2	19248	.	TAGA	TA	4.23339E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M2D1M;DP=17;DPB=16.5;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.4462;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=622;RO=16;RPL=1;RPP=5.18177;RPPR=22.5536;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=22.5536;SRR=14;TYPE=del;ANN=TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18987_18988delAG|p.Arg6329fs|18987/21291|18987/21291|6329/7096||INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1212_1213delAG|p.Arg404fs|1212/1581|1212/1581|404/526||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,TA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2313_-2312delGA|||||2313|,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-371_-370delGA|||||371|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1409_-1408delGA|||||1409|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3014_*3015delGA|||||3014|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1211_*1212delGA|||||1211|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:622:1:39:0,-1.22095,-52.4236

-NC_045512.2	19280	.	G	A	4.23339E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.4462;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=606;RO=16;RPL=0;RPP=5.18177;RPPR=29.6108;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=29.6108;SRR=15;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19016G>A|p.Cys6339Tyr|19016/21291|19016/21291|6339/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1241G>A|p.Cys414Tyr|1241/1581|1241/1581|414/526||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2283G>A|||||2283|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-341G>A|||||341|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1379G>A|||||1379|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3044G>A|||||3044|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1241G>A|||||1241|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:606:1:39:0,-1.22095,-50.9836

-NC_045512.2	19550	.	C	G	0.0198794	.	AB=0.166667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.38434;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=180;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19286C>G|p.Ala6429Gly|19286/21291|19286/21291|6429/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1511C>G|p.Ala504Gly|1511/1581|1511/1581|504/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2013C>G|||||2013|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-71C>G|||||71|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1109C>G|||||1109|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3314C>G|||||3314|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1511C>G|||||1511|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:5,1:5:180:1:34:-1.59273,0,-14.7444

-NC_045512.2	19718	.	C	T	49.3283	.	AB=0.285714;ABP=8.59409;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=11.6962;EPPR=16.9077;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.3582;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=390;RO=10;RPL=2;RPP=3.0103;RPPR=3.87889;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19454C>T|p.Thr6485Ile|19454/21291|19454/21291|6485/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.98C>T|p.Thr33Ile|98/1038|98/1038|33/345||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1845C>T|||||1845|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-941C>T|||||941|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3482C>T|||||3482|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1679C>T|||||1679|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*98C>T|||||98|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:14:10,4:10:390:4:156:-10.2029,0,-31.2443

-NC_045512.2	19848	.	T	G	2.83505E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=16.9077;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.9394;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=374;RO=10;RPL=0;RPP=5.18177;RPPR=10.8276;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=6.48466;SRR=7;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19584T>G|p.Gly6528Gly|19584/21291|19584/21291|6528/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.228T>G|p.Gly76Gly|228/1038|228/1038|76/345||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1715T>G|||||1715|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-811T>G|||||811|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3612T>G|||||3612|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1809T>G|||||1809|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*228T>G|||||228|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:11:10,1:10:374:1:33:0,-0.0121951,-30.71

-NC_045512.2	19859	.	C	T	7.09991E-5	.	AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=16.9077;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.0214;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=387;RO=10;RPL=0;RPP=5.18177;RPPR=10.8276;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=6.48466;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19595C>T|p.Ala6532Val|19595/21291|19595/21291|6532/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.239C>T|p.Ala80Val|239/1038|239/1038|80/345||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1704C>T|||||1704|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-800C>T|||||800|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3623C>T|||||3623|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1820C>T|||||1820|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*239C>T|||||239|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:10,1:10:387:1:37:-0.386499,0,-31.8762

-NC_045512.2	19869	.	T	C	3.24599E-4	.	AB=0.1;ABP=16.9077;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.50144;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=348;RO=9;RPL=1;RPP=5.18177;RPPR=5.18177;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=5.18177;SRR=6;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19605T>C|p.Thr6535Thr|19605/21291|19605/21291|6535/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.249T>C|p.Thr83Thr|249/1038|249/1038|83/345||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1694T>C|||||1694|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-790T>C|||||790|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3633T>C|||||3633|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1830T>C|||||1830|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*249T>C|||||249|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:9,1:9:348:1:38:-0.786969,0,-28.67

-NC_045512.2	20007	.	T	A	8.38126E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=5.18177;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.5528;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=150;RO=4;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19743T>A|p.Gly6581Gly|19743/21291|19743/21291|6581/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.387T>A|p.Gly129Gly|387/1038|387/1038|129/345||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1556T>A|||||1556|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-652T>A|||||652|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3771T>A|||||3771|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1968T>A|||||1968|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*387T>A|||||387|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5:4,1:4:150:1:15:0,-0.00516323,-12.3651

-NC_045512.2	20050	.	A	G	3.16558E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.52652;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=191;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19786A>G|p.Thr6596Ala|19786/21291|19786/21291|6596/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.430A>G|p.Thr144Ala|430/1038|430/1038|144/345||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1513A>G|||||1513|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-609A>G|||||609|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3814A>G|||||3814|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2011A>G|||||2011|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*430A>G|||||430|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:191:1:16:0,-0.206197,-15.9587

-NC_045512.2	20055	.	AGG	GGT	2.51455E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.75677;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=176;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=complex;ANN=GGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19791_19793delAGGinsGGT|p.Gly6598Val|19791/21291|19791/21291|6597/7096||,GGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.435_437delAGGinsGGT|p.Gly146Val|435/1038|435/1038|145/345||WARNING_TRANSCRIPT_NO_START_CODON,GGT|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1508_-1506delAGGinsGGT|||||1508|,GGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-604_-602delAGGinsGGT|||||604|WARNING_TRANSCRIPT_NO_START_CODON,GGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3819_*3821delAGGinsGGT|||||3819|WARNING_TRANSCRIPT_NO_START_CODON,GGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2016_*2018delAGGinsGGT|||||2016|WARNING_TRANSCRIPT_NO_START_CODON,GGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*435_*437delAGGinsGGT|||||435|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:176:1:15:0,-0.306193,-14.6818

-NC_045512.2	20064	.	T	A	3.16558E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.52652;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=161;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19800T>A|p.Val6600Val|19800/21291|19800/21291|6600/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.444T>A|p.Val148Val|444/1038|444/1038|148/345||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1499T>A|||||1499|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-595T>A|||||595|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3828T>A|||||3828|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2025T>A|||||2025|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*444T>A|||||444|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:161:1:16:0,-0.206197,-13.2023

-NC_045512.2	20078	.	CATC	ATTA	3.16558E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X1M1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.52652;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=175;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=complex;ANN=ATTA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19814_19817delCATCinsATTA|p.ProSer6605HisTyr|19814/21291|19814/21291|6605/7096||,ATTA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.458_461delCATCinsATTA|p.ProSer153HisTyr|458/1038|458/1038|153/345||WARNING_TRANSCRIPT_NO_START_CODON,ATTA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1485_-1482delCATCinsATTA|||||1485|,ATTA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-581_-578delCATCinsATTA|||||581|WARNING_TRANSCRIPT_NO_START_CODON,ATTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3842_*3845delCATCinsATTA|||||3842|WARNING_TRANSCRIPT_NO_START_CODON,ATTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2039_*2042delCATCinsATTA|||||2039|WARNING_TRANSCRIPT_NO_START_CODON,ATTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*458_*461delCATCinsATTA|||||458|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:175:1:16:0,-0.206197,-14.491

-NC_045512.2	20091	.	C	A	2.51455E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.75677;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=162;RO=5;RPL=0;RPP=5.18177;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=3.44459;SRR=2;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19827C>A|p.Pro6609Pro|19827/21291|19827/21291|6609/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.471C>A|p.Pro157Pro|471/1038|471/1038|157/345||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1472C>A|||||1472|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-568C>A|||||568|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3855C>A|||||3855|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2052C>A|||||2052|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*471C>A|||||471|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:162:1:15:0,-0.306193,-13.3948

-NC_045512.2	20113	.	GTCAC	TTCAT	0.025632	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X3M1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=5.13981;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=75;RO=2;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=complex;ANN=TTCAT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19849_19853delGTCACinsTTCAT|p.ValThr6617PheIle|19849/21291|19849/21291|6617/7096||,TTCAT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.493_497delGTCACinsTTCAT|p.ValThr165PheIle|493/1038|493/1038|165/345||WARNING_TRANSCRIPT_NO_START_CODON,TTCAT|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1450_-1446delGTCACinsTTCAT|||||1450|,TTCAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-546_-542delGTCACinsTTCAT|||||546|WARNING_TRANSCRIPT_NO_START_CODON,TTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3877_*3881delGTCACinsTTCAT|||||3877|WARNING_TRANSCRIPT_NO_START_CODON,TTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2074_*2078delGTCACinsTTCAT|||||2074|WARNING_TRANSCRIPT_NO_START_CODON,TTCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*493_*497delGTCACinsTTCAT|||||493|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:75:1:20:-1.09687,0,-6.21725

-NC_045512.2	20127	.	A	G	0.0101861	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.06079;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=77;RO=2;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19863A>G|p.Gly6621Gly|19863/21291|19863/21291|6621/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.507A>G|p.Gly169Gly|507/1038|507/1038|169/345||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1436A>G|||||1436|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-532A>G|||||532|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3891A>G|||||3891|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2088A>G|||||2088|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*507A>G|||||507|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:77:1:16:-0.696893,0,-6.40605

-NC_045512.2	20132	.	C	A	0.00810621	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.29104;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=76;RO=2;RPL=0;RPP=5.18177;RPPR=7.35324;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19868C>A|p.Ala6623Asp|19868/21291|19868/21291|6623/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.512C>A|p.Ala171Asp|512/1038|512/1038|171/345||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1431C>A|||||1431|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-527C>A|||||527|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3896C>A|||||3896|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2093C>A|||||2093|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*512C>A|||||512|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:76:1:15:-0.596897,0,-6.31172

-NC_045512.2	20195	.	C	A	3.3211E-5	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7812;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=269;RO=7;RPL=1;RPP=5.18177;RPPR=5.80219;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.80219;SRR=2;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19931C>A|p.Thr6644Asn|19931/21291|19931/21291|6644/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.575C>A|p.Thr192Asn|575/1038|575/1038|192/345||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1368C>A|||||1368|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-464C>A|||||464|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3959C>A|||||3959|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2156C>A|||||2156|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*575C>A|||||575|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:8:7,1:7:269:1:17:0,-0.708261,-22.8748

-NC_045512.2	20571	.	T	G	3.71119E-4	.	AB=0.111111;ABP=14.8328;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=5.18177;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.3675;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=296;RO=8;RPL=1;RPP=5.18177;RPPR=4.09604;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.09604;SRR=3;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20307T>G|p.Val6769Val|20307/21291|20307/21291|6769/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.951T>G|p.Val317Val|951/1038|951/1038|317/345||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-992T>G|||||992|,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4822T>G|||||4822|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-88T>G|||||88|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4335T>G|||||4335|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2532T>G|||||2532|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*951T>G|||||951|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:9:8,1:8:296:1:33:-0.589865,0,-24.2827

-NC_045512.2	20798	.	ATA	AA	2.30045E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=24;DPB=23.6667;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.2631;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=858;RO=23;RPL=0;RPP=5.18177;RPPR=14.4341;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=14.4341;SRR=6;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20535delT|p.Tyr6845fs|20535/21291|20535/21291|6845/7096||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.141delT|p.Tyr47fs|141/894|141/894|47/297||WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-764delT|||||764|,AA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4594delT|||||4594|,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4563delT|||||4563|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2760delT|||||2760|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1179delT|||||1179|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*141delT|||||141|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:858:1:37:0,-3.52689,-73.846

-NC_045512.2	21029	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.5538;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1359;RO=35;RPL=1;RPP=5.18177;RPPR=3.07234;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20765G>A|p.Trp6922*|20765/21291|20765/21291|6922/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.371G>A|p.Trp124*|371/894|371/894|124/297||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-534G>A|||||534|,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4364G>A|||||4364|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4793G>A|||||4793|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2990G>A|||||2990|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1409G>A|||||1409|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*371G>A|||||371|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1359:1:15:0,-9.33709,-121.093

-NC_045512.2	21255	.	G	C	186.146	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=16.0391;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=12.9229;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=234;QR=0;RO=0;RPL=3;RPP=3.0103;RPPR=0;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20991G>C|p.Ala6997Ala|20991/21291|20991/21291|6997/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.597G>C|p.Ala199Ala|597/894|597/894|199/297||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-308G>C|||||308|,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4138G>C|||||4138|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4990G>C|||||4990|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3216G>C|||||3216|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1635G>C|||||1635|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*597G>C|||||597|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:6:0,6:0:0:6:234:-21.4311,-1.80618,0

-NC_045512.2	21438	.	GTC	GC	3.21129	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M1D1M;DP=8;DPB=7.33333;DPRA=0;EPP=7.35324;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.0905122;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=225;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=5;SRP=8.80089;SRR=1;TYPE=del;ANN=GC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21175delT|p.Ser7059fs|21175/21291|21175/21291|7059/7096||,GC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.781delT|p.Ser261fs|781/894|781/894|261/297||WARNING_TRANSCRIPT_NO_START_CODON,GC|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-124delT|||||124|,GC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3954delT|||||3954|,GC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4806delT|||||4806|,GC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3400delT|||||3400|WARNING_TRANSCRIPT_NO_START_CODON,GC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1819delT|||||1819|WARNING_TRANSCRIPT_NO_START_CODON,GC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*781delT|||||781|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:6,2:6:225:2:76:-4.80657,0,-18.2012

-NC_045512.2	21614	.	C	T	0.204027	.	AB=0.2;ABP=6.91895;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=5.18177;EPPR=11.6962;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.03447;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=156;RO=4;RPL=0;RPP=5.18177;RPPR=11.6962;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=11.6962;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.52C>T|p.Leu18Phe|52/3822|52/3822|18/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3779C>T|||||3779|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4631C>T|||||4631|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4909C>T|||||4909|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*59C>T|||||59|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3575C>T|||||3575|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1994C>T|||||1994|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*956C>T|||||956|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*62C>T|||||62|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5:4,1:4:156:1:39:-2.39141,0,-12.9121

-NC_045512.2	21660	.	C	A	2.25009E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3808;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=585;RO=17;RPL=0;RPP=5.18177;RPPR=9.26925;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=9.26925;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.98C>A|p.Thr33Lys|98/3822|98/3822|33/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3733C>A|||||3733|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4585C>A|||||4585|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4863C>A|||||4863|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*105C>A|||||105|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3621C>A|||||3621|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2040C>A|||||2040|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1002C>A|||||1002|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*108C>A|||||108|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:585:1:32:0,-2.21923,-49.7715

-NC_045512.2	21673	.	T	C	8.86988E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.9193;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=836;RO=22;RPL=0;RPP=5.18177;RPPR=17.2236;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=17.2236;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.111T>C|p.Tyr37Tyr|111/3822|111/3822|37/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3720T>C|||||3720|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4572T>C|||||4572|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4850T>C|||||4850|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*118T>C|||||118|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3634T>C|||||3634|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2053T>C|||||2053|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1015T>C|||||1015|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*121T>C|||||121|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:836:1:37:0,-3.22586,-71.8673

-NC_045512.2	21718	.	G	T	2.09269E-8	.	AB=0.0833333;ABP=39.2015;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=7.35324;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.1508;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=79;QR=848;RO=22;RPL=0;RPP=7.35324;RPPR=17.2236;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=17;SRP=17.2236;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.156G>T|p.Gln52His|156/3822|156/3822|52/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3675G>T|||||3675|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4527G>T|||||4527|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4805G>T|||||4805|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*163G>T|||||163|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3679G>T|||||3679|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2098G>T|||||2098|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1060G>T|||||1060|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*166G>T|||||166|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:24:22,2:22:848:2:79:-0.272912,0,-69.4166

-NC_045512.2	21790	.	T	C	2.0055E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=7.35324;EPPR=66.2462;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6364;NS=1;NUMALT=1;ODDS=32.6796;PAIRED=1;PAIREDR=0.969697;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1274;RO=33;RPL=1;RPP=3.0103;RPPR=3.0761;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=18;SRP=3.60252;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.228T>C|p.Thr76Thr|228/3822|228/3822|76/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3603T>C|||||3603|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4455T>C|||||4455|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4733T>C|||||4733|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*235T>C|||||235|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3751T>C|||||3751|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2170T>C|||||2170|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1132T>C|||||1132|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*238T>C|||||238|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:33,2:33:1274:2:77:0,-3.22691,-107.599

-NC_045512.2	21839	.	G	T	4.51127E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=33.7915;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=1321;RO=34;RPL=1;RPP=3.0103;RPPR=3.26577;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=18;SRP=3.26577;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.277G>T|p.Ala93Ser|277/3822|277/3822|93/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3554G>T|||||3554|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4406G>T|||||4406|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4684G>T|||||4684|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*284G>T|||||284|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3800G>T|||||3800|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2219G>T|||||2219|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1181G>T|||||1181|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*287G>T|||||287|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,2:34:1321:2:78:0,-3.43361,-111.729

-NC_045512.2	21875	.	ATTTTTGGTA	ATTTTCGTA	2.2863E-7	.	AB=0.111111;ABP=50.3001;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1M1D4M1X3M;DP=36;DPB=35.6;DPRA=0;EPP=11.6962;EPPR=72.4974;GTI=0;LEN=9;MEANALT=1;MQM=60;MQMR=59.625;NS=1;NUMALT=1;ODDS=16.7597;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=148;QR=1208;RO=32;RPL=2;RPP=3.0103;RPPR=3.28173;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=17;SRP=3.28173;SRR=15;TYPE=complex;ANN=CGTA|frameshift_variant&synonymous_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.318_319delTGinsC|p.Gly107fs|318/3822|318/3822|106/1273||INFO_REALIGN_3_PRIME,CGTA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3513_-3509delTGGTAinsCGTA|||||3513|,CGTA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4365_-4361delTGGTAinsCGTA|||||4365|,CGTA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4643_-4639delTGGTAinsCGTA|||||4643|,CGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*325_*329delTGGTAinsCGTA|||||325|,CGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3841_*3845delTGGTAinsCGTA|||||3841|WARNING_TRANSCRIPT_NO_START_CODON,CGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2260_*2264delTGGTAinsCGTA|||||2260|WARNING_TRANSCRIPT_NO_START_CODON,CGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1222_*1226delTGGTAinsCGTA|||||1222|WARNING_TRANSCRIPT_NO_START_CODON,CGTA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*328_*332delTGGTAinsCGTA|||||328|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:36:32,4:32:1208:4:148:-2.84433,0,-98.1353

-NC_045512.2	21899	.	A	G	2.17751E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=50.0143;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1342;RO=35;RPL=1;RPP=5.18177;RPPR=3.07234;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.337A>G|p.Lys113Glu|337/3822|337/3822|113/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3494A>G|||||3494|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4346A>G|||||4346|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4624A>G|||||4624|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*344A>G|||||344|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3860A>G|||||3860|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2279A>G|||||2279|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1241A>G|||||1241|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*347A>G|||||347|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1342:1:13:0,-9.53709,-119.722

-NC_045512.2	21903	.	C	A	7.57925E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=48.8631;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=1354;RO=35;RPL=0;RPP=5.18177;RPPR=3.56868;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.56868;SRR=16;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.341C>A|p.Thr114Asn|341/3822|341/3822|114/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3490C>A|||||3490|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4342C>A|||||4342|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4620C>A|||||4620|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*348C>A|||||348|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3864C>A|||||3864|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2283C>A|||||2283|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1245C>A|||||1245|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*351C>A|||||351|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1354:1:18:0,-9.03711,-120.3

-NC_045512.2	21955	.	TGA	TA	1.36016E-4	.	AB=0.117647;ABP=24.5973;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M1D1M;DP=17;DPB=16.3333;DPRA=0;EPP=7.35324;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.2;NS=1;NUMALT=1;ODDS=10.3713;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=584;RO=15;RPL=2;RPP=7.35324;RPPR=35.5824;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=35.5824;SRR=15;TYPE=del;ANN=TA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.394delG|p.Glu132fs|394/3822|394/3822|132/1273||,TA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3437delG|||||3437|,TA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4289delG|||||4289|,TA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4567delG|||||4567|,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*401delG|||||401|,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3917delG|||||3917|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2336delG|||||2336|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1298delG|||||1298|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*404delG|||||404|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:17:15,2:15:584:2:78:-2.28596,0,-47.7422

-NC_045512.2	22018	.	G	C	3.76926E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6;NS=1;NUMALT=1;ODDS=41.6207;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=1149;RO=30;RPL=1;RPP=5.18177;RPPR=3.29983;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.29983;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.456G>C|p.Trp152Cys|456/3822|456/3822|152/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3375G>C|||||3375|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4227G>C|||||4227|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4505G>C|||||4505|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*463G>C|||||463|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3979G>C|||||3979|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2398G>C|||||2398|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1360G>C|||||1360|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*466G>C|||||466|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1149:1:20:0,-7.33197,-101.678

-NC_045512.2	22088	.	C	T	2.23124E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=4.51363;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.4815;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=502;RO=13;RPL=0;RPP=5.18177;RPPR=4.51363;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=31.2394;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.526C>T|p.Leu176Phe|526/3822|526/3822|176/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3305C>T|||||3305|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4157C>T|||||4157|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4435C>T|||||4435|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*533C>T|||||533|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4049C>T|||||4049|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2468C>T|||||2468|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1430C>T|||||1430|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*536C>T|||||536|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:502:1:39:0,-0.317855,-41.6316

-NC_045512.2	22227	.	C	T	470.255	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=17;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=31.7504;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=28.1722;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=662;QR=0;RO=0;RPL=17;RPP=39.9253;RPPR=0;RPR=0;RUN=1;SAF=1;SAP=31.7504;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.665C>T|p.Ala222Val|665/3822|665/3822|222/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3166C>T|||||3166|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4018C>T|||||4018|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4296C>T|||||4296|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4975C>T|||||4975|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*672C>T|||||672|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4188C>T|||||4188|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2607C>T|||||2607|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1569C>T|||||1569|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*675C>T|||||675|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:17:0,17:0:0:17:662:-59.9171,-5.11751,0

-NC_045512.2	22277	.	C	T	8.85446E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.9193;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=846;RO=22;RPL=0;RPP=5.18177;RPPR=12.8806;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=12.8806;SRR=16;TYPE=snp;ANN=T|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.715C>T|p.Gln239*|715/3822|715/3822|239/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3116C>T|||||3116|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3968C>T|||||3968|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4246C>T|||||4246|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4925C>T|||||4925|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*722C>T|||||722|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4238C>T|||||4238|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2657C>T|||||2657|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1619C>T|||||1619|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*725C>T|||||725|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:846:1:37:0,-3.22586,-72.7653

-NC_045512.2	22301	.	A	G	1.17513E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.2893;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18;QR=836;RO=22;RPL=1;RPP=5.18177;RPPR=9.32731;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=9.32731;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.739A>G|p.Ser247Gly|739/3822|739/3822|247/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3092A>G|||||3092|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3944A>G|||||3944|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4222A>G|||||4222|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4901A>G|||||4901|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*746A>G|||||746|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4262A>G|||||4262|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2681A>G|||||2681|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1643A>G|||||1643|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*749A>G|||||749|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:836:1:18:0,-5.12372,-73.7566

-NC_045512.2	22339	.	A	C	9.02856E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5195;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=820;RO=22;RPL=0;RPP=5.18177;RPPR=12.8806;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=12.8806;SRR=16;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.777A>C|p.Thr259Thr|777/3822|777/3822|259/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3054A>C|||||3054|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3906A>C|||||3906|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4184A>C|||||4184|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4863A>C|||||4863|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*784A>C|||||784|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4300A>C|||||4300|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2719A>C|||||2719|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1681A>C|||||1681|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*787A>C|||||787|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:820:1:17:0,-5.22371,-72.425

-NC_045512.2	22453	.	A	T	0.0791567	.	AB=0.153846;ABP=16.5402;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=7.35324;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.99575;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=407;RO=11;RPL=1;RPP=3.0103;RPPR=3.20771;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=3.20771;SRR=5;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.891A>T|p.Ser297Ser|891/3822|891/3822|297/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2940A>T|||||2940|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3792A>T|||||3792|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4070A>T|||||4070|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4749A>T|||||4749|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4941A>T|||||4941|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*898A>T|||||898|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4414A>T|||||4414|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2833A>T|||||2833|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1795A>T|||||1795|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*901A>T|||||901|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:13:11,2:11:407:2:78:-3.49008,0,-33.0554

-NC_045512.2	22484	.	G	A	0.0791567	.	AB=0.153846;ABP=16.5402;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=7.35324;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.99575;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=425;RO=11;RPL=1;RPP=3.0103;RPPR=3.20771;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=3.20771;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.922G>A|p.Val308Ile|922/3822|922/3822|308/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2909G>A|||||2909|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3761G>A|||||3761|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4039G>A|||||4039|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4718G>A|||||4718|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4910G>A|||||4910|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*929G>A|||||929|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4445G>A|||||4445|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2864G>A|||||2864|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1826G>A|||||1826|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*932G>A|||||932|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:13:11,2:11:425:2:78:-3.49008,0,-34.691

-NC_045512.2	22518	.	G	A	2.39065E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.7151;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=502;RO=14;RPL=0;RPP=5.18177;RPPR=33.4109;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=3.63072;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.956G>A|p.Arg319Lys|956/3822|956/3822|319/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2875G>A|||||2875|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3727G>A|||||3727|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4005G>A|||||4005|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4684G>A|||||4684|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4876G>A|||||4876|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*963G>A|||||963|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4479G>A|||||4479|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2898G>A|||||2898|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1860G>A|||||1860|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*966G>A|||||966|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:502:1:35:0,-1.01682,-42.0139

-NC_045512.2	22649	.	G	C	1.16513E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=18.9659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.9513;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=867;RO=23;RPL=1;RPP=5.18177;RPPR=10.6577;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=14.4341;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1087G>C|p.Ala363Pro|1087/3822|1087/3822|363/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2744G>C|||||2744|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3596G>C|||||3596|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3874G>C|||||3874|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4553G>C|||||4553|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4745G>C|||||4745|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1094G>C|||||1094|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4610G>C|||||4610|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3029G>C|||||3029|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1991G>C|||||1991|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1097G>C|||||1097|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:867:1:34:0,-3.82581,-74.9487

-NC_045512.2	22662	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=62.6327;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=44.2642;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1354;RO=35;RPL=0;RPP=5.18177;RPPR=4.56135;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1100T>C|p.Val367Ala|1100/3822|1100/3822|367/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2731T>C|||||2731|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3583T>C|||||3583|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3861T>C|||||3861|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4540T>C|||||4540|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4732T>C|||||4732|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1107T>C|||||1107|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4623T>C|||||4623|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3042T>C|||||3042|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2004T>C|||||2004|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1110T>C|||||1110|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1354:1:38:0,-7.03981,-118.304

-NC_045512.2	22740	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=70.5741;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=49.5538;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1336;RO=35;RPL=1;RPP=5.18177;RPPR=4.56135;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=3.56868;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1178C>T|p.Thr393Ile|1178/3822|1178/3822|393/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2653C>T|||||2653|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3505C>T|||||3505|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3783C>T|||||3783|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4462C>T|||||4462|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4654C>T|||||4654|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1185C>T|||||1185|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4701C>T|||||4701|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3120C>T|||||3120|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2082C>T|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1188C>T|||||1188|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1336:1:15:0,-9.33709,-118.977

-NC_045512.2	22791	.	T	A	1.02777E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=30.8051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.4;NS=1;NUMALT=1;ODDS=24.4669;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=728;RO=20;RPL=1;RPP=5.18177;RPPR=46.4397;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=30.8051;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1229T>A|p.Ile410Asn|1229/3822|1229/3822|410/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2602T>A|||||2602|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3454T>A|||||3454|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3732T>A|||||3732|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4411T>A|||||4411|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4603T>A|||||4603|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4965T>A|||||4965|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1236T>A|||||1236|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4752T>A|||||4752|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3171T>A|||||3171|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2133T>A|||||2133|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1239T>A|||||1239|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:728:1:36:0,-2.72335,-62.2055

-NC_045512.2	22859	.	G	A	1.24443E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=36.0395;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.3684;NS=1;NUMALT=1;ODDS=26.5795;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=709;RO=19;RPL=1;RPP=5.18177;RPPR=44.2683;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=36.0395;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1297G>A|p.Val433Ile|1297/3822|1297/3822|433/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2534G>A|||||2534|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3386G>A|||||3386|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3664G>A|||||3664|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4343G>A|||||4343|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4535G>A|||||4535|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4897G>A|||||4897|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1304G>A|||||1304|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4820G>A|||||4820|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3239G>A|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2201G>A|||||2201|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1307G>A|||||1307|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:19,1:19:709:1:21:0,-3.92065,-61.9884

-NC_045512.2	23126	.	G	C	1.34597E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5921;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=541;RO=16;RPL=0;RPP=5.18177;RPPR=37.7539;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=16;SRP=37.7539;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1564G>C|p.Ala522Pro|1564/3822|1564/3822|522/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2267G>C|||||2267|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3119G>C|||||3119|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3397G>C|||||3397|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4076G>C|||||4076|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4268G>C|||||4268|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4630G>C|||||4630|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4768G>C|||||4768|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1571G>C|||||1571|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3506G>C|||||3506|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2468G>C|||||2468|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1574G>C|||||1574|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:541:1:34:0,-1.7186,-45.6136

-NC_045512.2	23401	.	GGA	TGG,GGG	390.666	.	AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=1,15;CIGAR=1X1M1X,2M1X;DP=16;DPB=16;DPRA=0,0;EPP=5.18177,35.5824;EPPR=0;GTI=0;LEN=3,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=17.3492;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,585;QR=0;RO=0;RPL=1,15;RPP=5.18177,35.5824;RPPR=0;RPR=0,0;RUN=1,1;SAF=0,0;SAP=5.18177,35.5824;SAR=1,15;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=GGG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273||,TGG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1839_1841delGGAinsTGG|p.GlnAsp613HisGly|1839/3822|1839/3822|613/1273||,TGG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1992_-1990delGGAinsTGG|||||1992|,GGG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1990A>G|||||1990|,TGG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2844_-2842delGGAinsTGG|||||2844|,GGG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2842A>G|||||2842|,TGG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3122_-3120delGGAinsTGG|||||3122|,GGG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3120A>G|||||3120|,TGG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3801_-3799delGGAinsTGG|||||3801|,GGG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3799A>G|||||3799|,TGG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3993_-3991delGGAinsTGG|||||3993|,GGG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3991A>G|||||3991|,TGG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4355_-4353delGGAinsTGG|||||4355|,GGG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4353A>G|||||4353|,TGG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4493_-4491delGGAinsTGG|||||4493|,GGG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4491A>G|||||4491|,TGG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4873_-4871delGGAinsTGG|||||4873|,GGG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4871A>G|||||4871|,TGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1846_*1848delGGAinsTGG|||||1846|,GGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1848A>G|||||1848|,TGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3781_*3783delGGAinsTGG|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,GGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3783A>G|||||3783|WARNING_TRANSCRIPT_NO_START_CODON,TGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2743_*2745delGGAinsTGG|||||2743|WARNING_TRANSCRIPT_NO_START_CODON,GGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2745A>G|||||2745|WARNING_TRANSCRIPT_NO_START_CODON,TGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1849_*1851delGGAinsTGG|||||1849|WARNING_TRANSCRIPT_NO_START_CODON,GGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1851A>G|||||1851|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	2/2:16:0,1,15:0:0:1,15:38,585:-52.6129,-49.497,-49.196,-4.51545,-1.01921,0

-NC_045512.2	23422	.	C	T	1.59375E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.1206;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=570;RO=15;RPL=1;RPP=5.18177;RPPR=35.5824;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=35.5824;SRR=15;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1860C>T|p.Val620Val|1860/3822|1860/3822|620/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1971C>T|||||1971|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2823C>T|||||2823|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3101C>T|||||3101|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3780C>T|||||3780|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3972C>T|||||3972|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4334C>T|||||4334|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4472C>T|||||4472|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4852C>T|||||4852|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1867C>T|||||1867|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3802C>T|||||3802|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2764C>T|||||2764|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1870C>T|||||1870|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:570:1:39:0,-0.919915,-47.7463

-NC_045512.2	23445	.	A	C	7.0029E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=7.35324;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.2455;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=785;RO=21;RPL=0;RPP=7.35324;RPPR=15.5221;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=15.5221;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1883A>C|p.Gln628Pro|1883/3822|1883/3822|628/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1948A>C|||||1948|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2800A>C|||||2800|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3078A>C|||||3078|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3757A>C|||||3757|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3949A>C|||||3949|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4311A>C|||||4311|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4449A>C|||||4449|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4829A>C|||||4829|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1890A>C|||||1890|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3825A>C|||||3825|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2787A>C|||||2787|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1893A>C|||||1893|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:21,2:21:785:2:68:0,-0.465759,-64.5145

-NC_045512.2	23447	.	CTTAC	CTAC	1.16512E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=24;DPB=23.8;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.9513;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=858;RO=23;RPL=0;RPP=5.18177;RPPR=7.63648;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=7.63648;SRR=15;TYPE=del;ANN=CTAC|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1887delT|p.Thr630fs|1887/3822|1887/3822|629/1273||,CTAC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1944delT|||||1944|,CTAC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2796delT|||||2796|,CTAC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3074delT|||||3074|,CTAC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3753delT|||||3753|,CTAC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3945delT|||||3945|,CTAC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4307delT|||||4307|,CTAC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4445delT|||||4445|,CTAC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4825delT|||||4825|,CTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1894delT|||||1894|,CTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3829delT|||||3829|WARNING_TRANSCRIPT_NO_START_CODON,CTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2791delT|||||2791|WARNING_TRANSCRIPT_NO_START_CODON,CTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1897delT|||||1897|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:858:1:34:0,-3.82581,-74.1409

-NC_045512.2	23458	.	T	C	2.15846E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1020;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1896T>C|p.Thr632Thr|1896/3822|1896/3822|632/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1935T>C|||||1935|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2787T>C|||||2787|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3065T>C|||||3065|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3744T>C|||||3744|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3936T>C|||||3936|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4298T>C|||||4298|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4436T>C|||||4436|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4816T>C|||||4816|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1903T>C|||||1903|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3838T>C|||||3838|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2800T>C|||||2800|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1906T>C|||||1906|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1020:1:34:0,-5.02993,-88.7153

-NC_045512.2	23476	.	A	T	2.91109E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1965;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1048;RO=27;RPL=1;RPP=5.18177;RPPR=3.09072;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.09072;SRR=13;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1914A>T|p.Thr638Thr|1914/3822|1914/3822|638/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1917A>T|||||1917|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2769A>T|||||2769|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3047A>T|||||3047|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3726A>T|||||3726|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3918A>T|||||3918|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4280A>T|||||4280|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4418A>T|||||4418|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4798A>T|||||4798|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1921A>T|||||1921|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3856A>T|||||3856|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2818A>T|||||2818|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1924A>T|||||1924|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1048:1:39:0,-4.53228,-90.7299

-NC_045512.2	23511	.	TAATAG	TATAG,TAATAAG	9.25156E-14	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1M1D4M,4M1I2M;DP=27;DPB=27;DPRA=0,0;EPP=5.18177,5.18177;EPPR=57.2971;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=32.2084;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=34,35;QR=919;RO=25;RPL=1,1;RPP=5.18177,5.18177;RPPR=3.79203;RPR=0,0;RUN=1,1;SAF=0,0;SAP=5.18177,5.18177;SAR=1,1;SRF=14;SRP=3.79203;SRR=11;TYPE=del,ins;ANN=TATAG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1951delA|p.Ile651fs|1951/3822|1951/3822|651/1273||,TAATAAG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1953dupA|p.Gly652fs|1954/3822|1954/3822|652/1273||,TATAG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1880delA|||||1880|,TAATAAG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1878dupA|||||1877|,TATAG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2732delA|||||2732|,TAATAAG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2730dupA|||||2729|,TATAG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3010delA|||||3010|,TAATAAG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3008dupA|||||3007|,TATAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3689delA|||||3689|,TAATAAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3687dupA|||||3686|,TATAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3881delA|||||3881|,TAATAAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3879dupA|||||3878|,TATAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4243delA|||||4243|,TAATAAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4241dupA|||||4240|,TATAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4381delA|||||4381|,TAATAAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4379dupA|||||4378|,TATAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4761delA|||||4761|,TAATAAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4759dupA|||||4758|,TATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1958delA|||||1958|,TAATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1960dupA|||||1961|,TATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3893delA|||||3893|WARNING_TRANSCRIPT_NO_START_CODON,TAATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3895dupA|||||3896|WARNING_TRANSCRIPT_NO_START_CODON,TATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2855delA|||||2855|WARNING_TRANSCRIPT_NO_START_CODON,TAATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2857dupA|||||2858|WARNING_TRANSCRIPT_NO_START_CODON,TATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1961delA|||||1961|WARNING_TRANSCRIPT_NO_START_CODON,TAATAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1963dupA|||||1964|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:25,1,1:25:919:1,1:34,35:0,-4.77275,-79.6227,-4.67303,-77.0767,-79.5326

-NC_045512.2	23519	.	G	C	2.80594E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.0672;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=802;RO=22;RPL=1;RPP=5.18177;RPPR=6.56362;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=6.56362;SRR=8;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1957G>C|p.Ala653Pro|1957/3822|1957/3822|653/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1874G>C|||||1874|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2726G>C|||||2726|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3004G>C|||||3004|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3683G>C|||||3683|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3875G>C|||||3875|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4237G>C|||||4237|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4375G>C|||||4375|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4755G>C|||||4755|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1964G>C|||||1964|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3899G>C|||||3899|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2861G>C|||||2861|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1967G>C|||||1967|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:802:1:32:0,-3.72438,-69.3031

-NC_045512.2	23520	.	C	G	1.35316E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.4955;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=764;RO=21;RPL=1;RPP=5.18177;RPPR=8.07707;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=8.07707;SRR=7;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1958C>G|p.Ala653Gly|1958/3822|1958/3822|653/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1873C>G|||||1873|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2725C>G|||||2725|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3003C>G|||||3003|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3682C>G|||||3682|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3874C>G|||||3874|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4236C>G|||||4236|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4374C>G|||||4374|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4754C>G|||||4754|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1965C>G|||||1965|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3900C>G|||||3900|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2862C>G|||||2862|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1968C>G|||||1968|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:764:1:33:0,-3.32352,-65.784

-NC_045512.2	23521	.	T	G	4.10328E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.3856;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=736;RO=20;RPL=1;RPP=5.18177;RPPR=9.95901;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=9.95901;SRR=6;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1959T>G|p.Ala653Ala|1959/3822|1959/3822|653/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1872T>G|||||1872|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2724T>G|||||2724|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3002T>G|||||3002|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3681T>G|||||3681|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3873T>G|||||3873|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4235T>G|||||4235|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4373T>G|||||4373|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4753T>G|||||4753|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1966T>G|||||1966|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3901T>G|||||3901|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2863T>G|||||2863|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1969T>G|||||1969|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:736:1:32:0,-3.12232,-63.368

-NC_045512.2	23807	.	T	C	2.31586E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.2631;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=883;RO=23;RPL=0;RPP=5.18177;RPPR=10.6577;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=10.6577;SRR=16;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2245T>C|p.Cys749Arg|2245/3822|2245/3822|749/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1586T>C|||||1586|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2438T>C|||||2438|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2716T>C|||||2716|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3395T>C|||||3395|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3587T>C|||||3587|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3949T>C|||||3949|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4087T>C|||||4087|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4467T>C|||||4467|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2252T>C|||||2252|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4187T>C|||||4187|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3149T>C|||||3149|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2255T>C|||||2255|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:883:1:37:0,-3.52689,-76.0926

-NC_045512.2	23809	.	C	T	3.65676E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8055;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=885;RO=23;RPL=1;RPP=5.18177;RPPR=7.63648;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=7.63648;SRR=15;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2247C>T|p.Cys749Cys|2247/3822|2247/3822|749/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1584C>T|||||1584|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2436C>T|||||2436|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2714C>T|||||2714|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3393C>T|||||3393|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3585C>T|||||3585|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3947C>T|||||3947|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4085C>T|||||4085|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4465C>T|||||4465|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2254C>T|||||2254|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4189C>T|||||4189|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3151C>T|||||3151|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2257C>T|||||2257|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:885:1:39:0,-3.32816,-76.0739

-NC_045512.2	23812	.	C	T	3.65676E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8055;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=885;RO=23;RPL=1;RPP=5.18177;RPPR=7.63648;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=7.63648;SRR=15;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2250C>T|p.Ser750Ser|2250/3822|2250/3822|750/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1581C>T|||||1581|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2433C>T|||||2433|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2711C>T|||||2711|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3390C>T|||||3390|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3582C>T|||||3582|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3944C>T|||||3944|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4082C>T|||||4082|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4462C>T|||||4462|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2257C>T|||||2257|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4192C>T|||||4192|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3154C>T|||||3154|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2260C>T|||||2260|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:885:1:39:0,-3.32816,-76.0735

-NC_045512.2	24089	.	GAT	GT	1.96639E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=20;DPB=19.6667;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.8182;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=696;RO=19;RPL=0;RPP=5.18177;RPPR=4.03889;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=4.03889;SRR=8;TYPE=del;ANN=GT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2528delA|p.Asp843fs|2528/3822|2528/3822|843/1273||,GT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1303delA|||||1303|,GT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2155delA|||||2155|,GT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2433delA|||||2433|,GT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3112delA|||||3112|,GT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3304delA|||||3304|,GT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3666delA|||||3666|,GT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3804delA|||||3804|,GT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4184delA|||||4184|,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2535delA|||||2535|,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4470delA|||||4470|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3432delA|||||3432|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2538delA|||||2538|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:19,1:19:696:1:33:0,-2.72146,-59.669

-NC_045512.2	24158	.	ACA	AA	1.87129E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=19;DPB=18.6667;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.5652;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=688;RO=18;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=12;SRP=7.35324;SRR=6;TYPE=del;ANN=AA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2597delC|p.Thr866fs|2597/3822|2597/3822|866/1273||,AA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1234delC|||||1234|,AA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2086delC|||||2086|,AA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2364delC|||||2364|,AA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3043delC|||||3043|,AA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3235delC|||||3235|,AA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3597delC|||||3597|,AA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3735delC|||||3735|,AA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4115delC|||||4115|,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2604delC|||||2604|,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4539delC|||||4539|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3501delC|||||3501|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2607delC|||||2607|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:688:1:37:0,-2.02174,-58.556

-NC_045512.2	24222	.	C	A	5.42345E-8	.	AB=0.0833333;ABP=39.2015;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=7.35324;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.1985;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=853;RO=22;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2660C>A|p.Thr887Asn|2660/3822|2660/3822|887/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1171C>A|||||1171|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2023C>A|||||2023|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2301C>A|||||2301|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2980C>A|||||2980|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3172C>A|||||3172|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3534C>A|||||3534|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3672C>A|||||3672|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4052C>A|||||4052|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2667C>A|||||2667|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4602C>A|||||4602|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3564C>A|||||3564|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2670C>A|||||2670|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:24:22,2:22:853:2:77:-0.0844219,0,-69.8677

-NC_045512.2	24334	.	CAACCAA	TAACAA,TAACCAA	306.141	.	AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=1,11;CIGAR=1X2M1D3M,1X6M;DP=12;DPB=12.1429;DPRA=0,0;EPP=5.18177,19.0002;EPPR=0;GTI=0;LEN=6,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=14.6357;PAIRED=1,1;PAIREDR=0;PAO=1,1;PQA=37.5,37.5;PQR=0;PRO=0;QA=39,429;QR=0;RO=0;RPL=0,1;RPP=5.18177,19.0002;RPPR=0;RPR=1,10;RUN=1,1;SAF=0,0;SAP=5.18177,26.8965;SAR=1,11;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=TAACAA|frameshift_variant&synonymous_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2772_2775delCAACinsTAA|p.Asn925fs|2772/3822|2772/3822|924/1273||INFO_REALIGN_3_PRIME,TAACCAA|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2772C>T|p.Ala924Ala|2772/3822|2772/3822|924/1273||,TAACCAA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1059C>T|||||1059|,TAACAA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1059_-1053delCAACCAAinsTAACAA|||||1059|,TAACCAA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1911C>T|||||1911|,TAACAA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1911_-1905delCAACCAAinsTAACAA|||||1911|,TAACCAA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2189C>T|||||2189|,TAACAA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2189_-2183delCAACCAAinsTAACAA|||||2189|,TAACCAA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2868C>T|||||2868|,TAACAA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2868_-2862delCAACCAAinsTAACAA|||||2868|,TAACCAA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3060C>T|||||3060|,TAACAA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3060_-3054delCAACCAAinsTAACAA|||||3060|,TAACCAA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3422C>T|||||3422|,TAACAA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3422_-3416delCAACCAAinsTAACAA|||||3422|,TAACCAA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3560C>T|||||3560|,TAACAA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3560_-3554delCAACCAAinsTAACAA|||||3560|,TAACCAA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3940C>T|||||3940|,TAACAA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3940_-3934delCAACCAAinsTAACAA|||||3940|,TAACCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2779C>T|||||2779|,TAACAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2779_*2785delCAACCAAinsTAACAA|||||2779|,TAACCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4714C>T|||||4714|WARNING_TRANSCRIPT_NO_START_CODON,TAACAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4714_*4720delCAACCAAinsTAACAA|||||4714|WARNING_TRANSCRIPT_NO_START_CODON,TAACCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3676C>T|||||3676|WARNING_TRANSCRIPT_NO_START_CODON,TAACAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3676_*3682delCAACCAAinsTAACAA|||||3676|WARNING_TRANSCRIPT_NO_START_CODON,TAACCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2782C>T|||||2782|WARNING_TRANSCRIPT_NO_START_CODON,TAACAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2782_*2788delCAACCAAinsTAACAA|||||2782|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	2/2:12:0,1,11:0:0:1,11:39,429:-38.4653,-36.5742,-35.0691,-4.51545,-0.919916,0

-NC_045512.2	24491	.	T	A	3.05998E-5	.	AB=0.0833333;ABP=21.1059;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.8631;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=428;RO=11;RPL=0;RPP=5.18177;RPPR=26.8965;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=26.8965;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2929T>A|p.Leu977Ile|2929/3822|2929/3822|977/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-902T>A|||||902|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1754T>A|||||1754|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2032T>A|||||2032|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2711T>A|||||2711|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2903T>A|||||2903|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3265T>A|||||3265|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3403T>A|||||3403|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3783T>A|||||3783|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2936T>A|||||2936|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4871T>A|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3833T>A|||||3833|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2939T>A|||||2939|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:11,1:11:428:1:39:-0.284205,0,-35.263

-NC_045512.2	24653	.	G	T	1.12198E-4	.	AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.5638;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=390;RO=10;RPL=0;RPP=5.18177;RPPR=16.9077;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=16.9077;SRR=9;TYPE=snp;ANN=T|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3091G>T|p.Glu1031*|3091/3822|3091/3822|1031/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-740G>T|||||740|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1592G>T|||||1592|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1870G>T|||||1870|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2549G>T|||||2549|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2741G>T|||||2741|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3103G>T|||||3103|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3241G>T|||||3241|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3621G>T|||||3621|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4905G>T|||||4905|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3098G>T|||||3098|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3995G>T|||||3995|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3101G>T|||||3101|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:10,1:10:390:1:39:-0.585235,0,-32.1474

-NC_045512.2	24655	.	G	T	8.92671E-5	.	AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.7924;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=376;RO=10;RPL=0;RPP=5.18177;RPPR=16.9077;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=16.9077;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3093G>T|p.Glu1031Asp|3093/3822|3093/3822|1031/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-738G>T|||||738|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1590G>T|||||1590|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1868G>T|||||1868|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2547G>T|||||2547|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2739G>T|||||2739|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3101G>T|||||3101|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3239G>T|||||3239|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3619G>T|||||3619|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4903G>T|||||4903|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3100G>T|||||3100|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3997G>T|||||3997|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3103G>T|||||3103|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:10,1:10:376:1:38:-0.485939,0,-30.8816

-NC_045512.2	24658	.	T	G	2.84066E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.5426;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=389;RO=10;RPL=1;RPP=5.18177;RPPR=24.725;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=0;SRP=24.725;SRR=10;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3096T>G|p.Cys1032Trp|3096/3822|3096/3822|1032/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-735T>G|||||735|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1587T>G|||||1587|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1865T>G|||||1865|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2544T>G|||||2544|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2736T>G|||||2736|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3098T>G|||||3098|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3236T>G|||||3236|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3616T>G|||||3616|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4900T>G|||||4900|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3103T>G|||||3103|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4000T>G|||||4000|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3106T>G|||||3106|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:11:10,1:10:389:1:13:0,-2.01134,-34.0684

-NC_045512.2	24703	.	T	A	2.8418E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.046;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1082;RO=29;RPL=0;RPP=5.18177;RPPR=9.07545;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=9.07545;SRR=10;TYPE=snp;ANN=A|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3141T>A|p.Tyr1047*|3141/3822|3141/3822|1047/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-690T>A|||||690|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1542T>A|||||1542|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1820T>A|||||1820|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2499T>A|||||2499|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2691T>A|||||2691|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3053T>A|||||3053|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3191T>A|||||3191|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3571T>A|||||3571|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4855T>A|||||4855|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3148T>A|||||3148|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4045T>A|||||4045|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3151T>A|||||3151|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1082:1:34:0,-5.63199,-94.2896

-NC_045512.2	24714	.	C	T	4.42237E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.0657;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1175;RO=31;RPL=0;RPP=5.18177;RPPR=11.486;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=11.486;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3152C>T|p.Ser1051Phe|3152/3822|3152/3822|1051/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-679C>T|||||679|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1531C>T|||||1531|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1809C>T|||||1809|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2488C>T|||||2488|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2680C>T|||||2680|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3042C>T|||||3042|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3180C>T|||||3180|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3560C>T|||||3560|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4844C>T|||||4844|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3159C>T|||||3159|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4056C>T|||||4056|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3162C>T|||||3162|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1175:1:37:0,-5.93513,-102.356

-NC_045512.2	24789	.	C	G	2.91109E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1965;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1022;RO=27;RPL=0;RPP=5.18177;RPPR=26.2531;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=26.2531;SRR=5;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3227C>G|p.Thr1076Arg|3227/3822|3227/3822|1076/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-604C>G|||||604|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1456C>G|||||1456|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1734C>G|||||1734|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2413C>G|||||2413|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2605C>G|||||2605|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2967C>G|||||2967|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3105C>G|||||3105|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3485C>G|||||3485|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4769C>G|||||4769|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3234C>G|||||3234|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4131C>G|||||4131|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3237C>G|||||3237|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1022:1:39:0,-4.53228,-88.3906

-NC_045512.2	24890	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=7.35324;EPPR=92.2337;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.8313;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=49;QR=1751;RO=45;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=22;SRP=3.05855;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3328T>A|p.Tyr1110Asn|3328/3822|3328/3822|1110/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-503T>A|||||503|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1355T>A|||||1355|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1633T>A|||||1633|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2312T>A|||||2312|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2504T>A|||||2504|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2866T>A|||||2866|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3004T>A|||||3004|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3384T>A|||||3384|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4668T>A|||||4668|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3335T>A|||||3335|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4232T>A|||||4232|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3338T>A|||||3338|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:47:45,2:45:1751:2:49:0,-9.49425,-153.188

-NC_045512.2	24980	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=72.7387;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.77;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1329;RO=36;RPL=0;RPP=5.18177;RPPR=14.8328;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=12;SRP=11.6962;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3418C>T|p.Pro1140Ser|3418/3822|3418/3822|1140/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-413C>T|||||413|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1265C>T|||||1265|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1543C>T|||||1543|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2222C>T|||||2222|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2414C>T|||||2414|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2776C>T|||||2776|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2914C>T|||||2914|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3294C>T|||||3294|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4578C>T|||||4578|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3425C>T|||||3425|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4322C>T|||||4322|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3428C>T|||||3428|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1329:1:33:0,-7.83897,-116.599

-NC_045512.2	24991	.	T	C	1.31392E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=5.18177;EPPR=79.2345;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.704;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1499;RO=39;RPL=1;RPP=5.18177;RPPR=7.52028;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=5.73856;SRR=23;TYPE=snp;ANN=C|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3429T>C|p.Pro1143Pro|3429/3822|3429/3822|1143/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-402T>C|||||402|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1254T>C|||||1254|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1532T>C|||||1532|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2211T>C|||||2211|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2403T>C|||||2403|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2765T>C|||||2765|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2903T>C|||||2903|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3283T>C|||||3283|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4567T>C|||||4567|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3436T>C|||||3436|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4333T>C|||||4333|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3439T>C|||||3439|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1499:1:38:0,-8.24393,-131.389

-NC_045512.2	25012	.	G	C	7.39672E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=9.52472;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.9749;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=117;QR=1422;RO=37;RPL=0;RPP=9.52472;RPPR=12.9286;RPR=3;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=13;SRP=10.1116;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3450G>C|p.Glu1150Asp|3450/3822|3450/3822|1150/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-381G>C|||||381|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1233G>C|||||1233|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1511G>C|||||1511|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2190G>C|||||2190|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2382G>C|||||2382|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2744G>C|||||2744|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2882G>C|||||2882|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3262G>C|||||3262|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4546G>C|||||4546|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3457G>C|||||3457|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4354G>C|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3460G>C|||||3460|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:37,3:37:1422:3:117:0,-1.13082,-117.34

-NC_045512.2	25035	.	A	G	9.71908E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.343;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1476;RO=38;RPL=1;RPP=5.18177;RPPR=6.66752;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=6.66752;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3473A>G|p.Asn1158Ser|3473/3822|3473/3822|1158/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-358A>G|||||358|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1210A>G|||||1210|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1488A>G|||||1488|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2167A>G|||||2167|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2359A>G|||||2359|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2721A>G|||||2721|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2859A>G|||||2859|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3239A>G|||||3239|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4523A>G|||||4523|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3480A>G|||||3480|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4377A>G|||||4377|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3483A>G|||||3483|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1476:1:38:0,-7.9429,-129.317

-NC_045512.2	25067	.	ATCT	AT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M2D1M;DP=34;DPB=33.5;DPRA=0;EPP=5.18177;EPPR=74.6689;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.7777;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1207;RO=33;RPL=1;RPP=5.18177;RPPR=3.60252;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.60252;SRR=18;TYPE=del;ANN=AT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3509_3510delCT|p.Ser1170fs|3509/3822|3509/3822|1170/1273||INFO_REALIGN_3_PRIME,AT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-324_-323delCT|||||324|,AT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1176_-1175delCT|||||1176|,AT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1454_-1453delCT|||||1454|,AT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2133_-2132delCT|||||2133|,AT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2325_-2324delCT|||||2325|,AT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2687_-2686delCT|||||2687|,AT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2825_-2824delCT|||||2825|,AT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3205_-3204delCT|||||3205|,AT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4489_-4488delCT|||||4489|,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3514_*3515delCT|||||3514|,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4411_*4412delCT|||||4411|WARNING_TRANSCRIPT_NO_START_CODON,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3517_*3518delCT|||||3517|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:34:33,1:33:1207:1:37:0,-6.53719,-105.231

-NC_045512.2	25075	.	C	A	2.17051E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.5056;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1056;RO=29;RPL=1;RPP=5.18177;RPPR=3.08518;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=A|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3513C>A|p.Gly1171Gly|3513/3822|3513/3822|1171/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-318C>A|||||318|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1170C>A|||||1170|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1448C>A|||||1448|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2127C>A|||||2127|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2319C>A|||||2319|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2681C>A|||||2681|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2819C>A|||||2819|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3199C>A|||||3199|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4483C>A|||||4483|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3520C>A|||||3520|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4417C>A|||||4417|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3523C>A|||||3523|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1056:1:32:0,-5.83159,-92.1457

-NC_045512.2	25151	.	C	A	2.00854E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.4184;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1114;RO=29;RPL=0;RPP=5.18177;RPPR=3.08518;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3589C>A|p.Leu1197Ile|3589/3822|3589/3822|1197/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-242C>A|||||242|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1094C>A|||||1094|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1372C>A|||||1372|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2051C>A|||||2051|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2243C>A|||||2243|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2605C>A|||||2605|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2743C>A|||||2743|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3123C>A|||||3123|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4407C>A|||||4407|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3596C>A|||||3596|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4493C>A|||||4493|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3599C>A|||||3599|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1114:1:15:0,-7.53091,-99.0611

-NC_045512.2	25301	.	T	C	4.21917E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.3642;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1302;RO=34;RPL=0;RPP=5.18177;RPPR=4.03217;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=4.03217;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3739T>C|p.Cys1247Arg|3739/3822|3739/3822|1247/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-92T>C|||||92|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-944T>C|||||944|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1222T>C|||||1222|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1901T>C|||||1901|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2093T>C|||||2093|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2455T>C|||||2455|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2593T>C|||||2593|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2973T>C|||||2973|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4257T>C|||||4257|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3746T>C|||||3746|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4643T>C|||||4643|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3749T>C|||||3749|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:34,1:34:1302:1:36:0,-6.93777,-113.873

-NC_045512.2	25360	.	AGGAGT	AGAGT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D4M;DP=35;DPB=34.8333;DPRA=0;EPP=5.18177;EPPR=68.4099;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.135;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=1259;RO=34;RPL=1;RPP=5.18177;RPPR=12.2071;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=9.39698;SRR=12;TYPE=del;ANN=AGAGT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3800delG|p.Gly1267fs|3800/3822|3800/3822|1267/1273||,AGAGT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-31delG|||||31|,AGAGT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-883delG|||||883|,AGAGT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1161delG|||||1161|,AGAGT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1840delG|||||1840|,AGAGT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2032delG|||||2032|,AGAGT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2394delG|||||2394|,AGAGT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2532delG|||||2532|,AGAGT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2912delG|||||2912|,AGAGT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4196delG|||||4196|,AGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3807delG|||||3807|,AGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4704delG|||||4704|WARNING_TRANSCRIPT_NO_START_CODON,AGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3810delG|||||3810|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:34,1:34:1259:1:37:0,-6.83822,-109.91

-NC_045512.2	25426	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=81.9729;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8073;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1675;RO=44;RPL=0;RPP=5.18177;RPPR=3.79993;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0103;SRR=22;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.34A>T|p.Thr12Ser|34/828|34/828|12/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-819A>T|||||819|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1097A>T|||||1097|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1776A>T|||||1776|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1968A>T|||||1968|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2330A>T|||||2330|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2468A>T|||||2468|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2848A>T|||||2848|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4132A>T|||||4132|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3871A>T|||||3871|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*42A>T|||||42|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4768A>T|||||4768|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3874A>T|||||3874|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1675:1:15:0,-12.0464,-149.518

-NC_045512.2	25522	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=90.0666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.3468;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1654;RO=44;RPL=0;RPP=5.18177;RPPR=3.20771;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0103;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.130G>A|p.Gly44Arg|130/828|130/828|44/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-723G>A|||||723|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1001G>A|||||1001|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1680G>A|||||1680|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1872G>A|||||1872|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2234G>A|||||2234|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2372G>A|||||2372|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2752G>A|||||2752|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4036G>A|||||4036|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3967G>A|||||3967|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*138G>A|||||138|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4864G>A|||||4864|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3970G>A|||||3970|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1654:1:17:0,-11.8464,-147.421

-NC_045512.2	25542	.	T	G	1.78853E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=41.3151;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.7071;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=971;RO=25;RPL=1;RPP=5.18177;RPPR=28.1125;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=41.3151;SRR=23;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.150T>G|p.Val50Val|150/828|150/828|50/275||,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-703T>G|||||703|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-981T>G|||||981|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1660T>G|||||1660|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1852T>G|||||1852|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2214T>G|||||2214|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2352T>G|||||2352|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2732T>G|||||2732|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4016T>G|||||4016|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3987T>G|||||3987|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*158T>G|||||158|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4884T>G|||||4884|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3990T>G|||||3990|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:971:1:12:0,-6.62679,-86.5032

-NC_045512.2	25572	.	CAAAATC	CAAATC	1.1388E-5	.	AB=0.12;ABP=34.3664;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1M1D5M;DP=25;DPB=24.5714;DPRA=0;EPP=9.52472;EPPR=34.9902;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.8515;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=116;QR=843;RO=22;RPL=3;RPP=9.52472;RPPR=50.7827;RPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=2;SRP=34.9902;SRR=20;TYPE=del;ANN=CAAATC|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.184delA|p.Ile62fs|184/828|184/828|62/275||,CAAATC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-669delA|||||669|,CAAATC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-947delA|||||947|,CAAATC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1626delA|||||1626|,CAAATC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1818delA|||||1818|,CAAATC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2180delA|||||2180|,CAAATC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2318delA|||||2318|,CAAATC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2698delA|||||2698|,CAAATC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3982delA|||||3982|,CAAATC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4021delA|||||4021|,CAAATC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*192delA|||||192|,CAAATC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4918delA|||||4918|WARNING_TRANSCRIPT_NO_START_CODON,CAAATC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4024delA|||||4024|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF3a|GU280_gp03|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:25:22,3:22:843:3:116:-3.29195,0,-68.666

-NC_045512.2	25614	.	CAAG	CC	2.96509E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M2D1X;DP=25;DPB=24;DPRA=0;EPP=7.35324;EPPR=52.9542;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.1049;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=867;RO=23;RPL=2;RPP=7.35324;RPPR=30.2953;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=30.2953;SRR=20;TYPE=complex;ANN=C|frameshift_variant&missense_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.223_225delAAGinsC|p.Lys75fs|223/828|223/828|75/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-630_-628delAAGinsC|||||630|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-908_-906delAAGinsC|||||908|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1587_-1585delAAGinsC|||||1587|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1779_-1777delAAGinsC|||||1779|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2141_-2139delAAGinsC|||||2141|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2279_-2277delAAGinsC|||||2279|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2659_-2657delAAGinsC|||||2659|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3943_-3941delAAGinsC|||||3943|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4060_*4062delAAGinsC|||||4060|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*231_*233delAAGinsC|||||231|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4957_*4959delAAGinsC|||||4957|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4063_*4065delAAGinsC|||||4063|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF3a|GU280_gp03|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:23,2:23:867:2:76:0,-0.310939,-71.1377

-NC_045512.2	25672	.	C	T	7.83754E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.7381;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=29;QR=632;RO=19;RPL=1;RPP=5.18177;RPPR=16.8392;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=16.8392;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.280C>T|p.Leu94Phe|280/828|280/828|94/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-573C>T|||||573|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-851C>T|||||851|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1530C>T|||||1530|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1722C>T|||||1722|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2084C>T|||||2084|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2222C>T|||||2222|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2602C>T|||||2602|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3886C>T|||||3886|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4117C>T|||||4117|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*288C>T|||||288|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4120C>T|||||4120|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:19,1:19:632:1:29:0,-3.12094,-54.2919

-NC_045512.2	25906	.	G	C	8.19225E-5	.	AB=0.1;ABP=16.9077;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.8783;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=322;RO=9;RPL=0;RPP=5.18177;RPPR=3.25157;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.514G>C|p.Gly172Arg|514/828|514/828|172/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-339G>C|||||339|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-617G>C|||||617|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1296G>C|||||1296|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1488G>C|||||1488|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1850G>C|||||1850|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1988G>C|||||1988|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2368G>C|||||2368|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3652G>C|||||3652|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4351G>C|||||4351|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*522G>C|||||522|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4354G>C|||||4354|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:9,1:9:322:1:32:-0.189013,0,-26.3106

-NC_045512.2	25999	.	T	A	7.95066E-4	.	AB=0.166667;ABP=8.80089;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.60555;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=195;RO=5;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.607T>A|p.Leu203Ile|607/828|607/828|203/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-246T>A|||||246|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-524T>A|||||524|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1203T>A|||||1203|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1395T>A|||||1395|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1757T>A|||||1757|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1895T>A|||||1895|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2275T>A|||||2275|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3559T>A|||||3559|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4444T>A|||||4444|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*615T>A|||||615|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4447T>A|||||4447|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:5,1:5:195:1:20:-0.193777,0,-16.118

-NC_045512.2	26126	.	A	G	0.21231	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.99372;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=389;RO=10;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.734A>G|p.Gln245Arg|734/828|734/828|245/275||,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-119A>G|||||119|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-397A>G|||||397|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1076A>G|||||1076|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1268A>G|||||1268|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1630A>G|||||1630|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1768A>G|||||1768|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2148A>G|||||2148|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3432A>G|||||3432|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4571A>G|||||4571|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*742A>G|||||742|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4574A>G|||||4574|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:10,2:10:389:2:77:-3.69678,0,-31.756

-NC_045512.2	26152	.	G	T	0.21231	.	AB=0.166667;ABP=14.5915;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=7.35324;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.99372;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=381;RO=10;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=T|stop_gained|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.760G>T|p.Gly254*|760/828|760/828|254/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-93G>T|||||93|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-371G>T|||||371|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1050G>T|||||1050|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1242G>T|||||1242|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1604G>T|||||1604|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1742G>T|||||1742|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2122G>T|||||2122|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3406G>T|||||3406|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4597G>T|||||4597|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*768G>T|||||768|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4600G>T|||||4600|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:10,2:10:381:2:77:-3.69678,0,-31.0321

-NC_045512.2	26199	.	G	C	3.56286E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9213;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=597;RO=17;RPL=0;RPP=5.18177;RPPR=6.20364;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=6.20364;SRR=6;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.807G>C|p.Thr269Thr|807/828|807/828|269/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-46G>C|||||46|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-324G>C|||||324|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1003G>C|||||1003|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1195G>C|||||1195|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1557G>C|||||1557|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1695G>C|||||1695|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2075G>C|||||2075|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3359G>C|||||3359|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4644G>C|||||4644|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*815G>C|||||815|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4647G>C|||||4647|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:597:1:34:0,-2.01963,-50.6561

-NC_045512.2	26238	.	C	T	3.65676E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8055;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=888;RO=23;RPL=0;RPP=5.18177;RPPR=14.4341;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=14.4341;SRR=6;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-7C>T|||||7|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-285C>T|||||285|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-964C>T|||||964|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1156C>T|||||1156|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1518C>T|||||1518|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1656C>T|||||1656|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2036C>T|||||2036|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3320C>T|||||3320|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4683C>T|||||4683|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*854C>T|||||854|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*18C>T|||||18|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4686C>T|||||4686|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|ORF3a-E|GU280_gp03-GU280_gp04|intergenic_region|GU280_gp03-GU280_gp04|||n.26238C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:888:1:39:0,-3.32816,-76.3433

-NC_045512.2	26313	.	C	T	4.479E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=42.4916;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.6076;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=837;RO=22;RPL=1;RPP=5.18177;RPPR=28.2783;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=22.3561;SRR=4;TYPE=snp;ANN=T|synonymous_variant|LOW|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.69C>T|p.Phe23Phe|69/228|69/228|23/75||,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-210C>T|||||210|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-889C>T|||||889|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1081C>T|||||1081|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1443C>T|||||1443|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1581C>T|||||1581|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1961C>T|||||1961|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3245C>T|||||3245|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4758C>T|||||4758|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*929C>T|||||929|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*93C>T|||||93|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4761C>T|||||4761|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:837:1:34:0,-3.52478,-72.2521

-NC_045512.2	26424	.	T	C	161.596	.	AB=0.277778;ABP=18.4519;AC=1;AF=0.5;AN=2;AO=10;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=16.9077;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.2088;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=382;QR=991;RO=26;RPL=6;RPP=3.87889;RPPR=3.0103;RPR=4;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=C|synonymous_variant|LOW|E|GU280_gp04|transcript|GU280_gp04|protein_coding|1/1|c.180T>C|p.Ser60Ser|180/228|180/228|60/75||,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-99T>C|||||99|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-778T>C|||||778|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-970T>C|||||970|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1332T>C|||||1332|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1470T>C|||||1470|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1850T>C|||||1850|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3134T>C|||||3134|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4869T>C|||||4869|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1040T>C|||||1040|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*204T>C|||||204|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4872T>C|||||4872|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:36:26,10:26:991:10:382:-23.8988,0,-78.6679

-NC_045512.2	26542	.	CTAT	ATAG	4.41335E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.4822;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1130;RO=30;RPL=1;RPP=5.18177;RPPR=3.29983;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.29983;SRR=16;TYPE=complex;ANN=ATAG|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.20_23delCTATinsATAG|p.ThrIle7AsnSer|20/669|20/669|7/222||,ATAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-660_-657delCTATinsATAG|||||660|,ATAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-852_-849delCTATinsATAG|||||852|,ATAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1214_-1211delCTATinsATAG|||||1214|,ATAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1352_-1349delCTATinsATAG|||||1352|,ATAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1732_-1729delCTATinsATAG|||||1732|,ATAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3016_-3013delCTATinsATAG|||||3016|,ATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4987_*4990delCTATinsATAG|||||4987|,ATAG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1158_*1161delCTATinsATAG|||||1158|,ATAG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*322_*325delCTATinsATAG|||||322|,ATAG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*70_*73delCTATinsATAG|||||70|,ATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4990_*4993delCTATinsATAG|||||4990|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1130:1:38:0,-5.53466,-98.2084

-NC_045512.2	26561	.	T	A	4.41335E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.4822;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1154;RO=30;RPL=1;RPP=5.18177;RPPR=3.29983;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=3.29983;SRR=16;TYPE=snp;ANN=A|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.39T>A|p.Leu13Leu|39/669|39/669|13/222||,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-641T>A|||||641|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-833T>A|||||833|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1195T>A|||||1195|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1333T>A|||||1333|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1713T>A|||||1713|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2997T>A|||||2997|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1177T>A|||||1177|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*341T>A|||||341|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*89T>A|||||89|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1154:1:38:0,-5.53466,-100.362

-NC_045512.2	26626	.	T	C	1.12268E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.1683;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=507;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=31.2394;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.104T>C|p.Leu35Pro|104/669|104/669|35/222||,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-576T>C|||||576|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-768T>C|||||768|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1130T>C|||||1130|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1268T>C|||||1268|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1648T>C|||||1648|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2932T>C|||||2932|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1242T>C|||||1242|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*406T>C|||||406|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*154T>C|||||154|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:507:1:36:0,-0.616145,-42.3812

-NC_045512.2	26709	.	G	T	1.02766E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=7.35324;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.6968;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=966;RO=26;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=3.0103;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.187G>T|p.Ala63Ser|187/669|187/669|63/222||,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-493G>T|||||493|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-685G>T|||||685|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1047G>T|||||1047|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1185G>T|||||1185|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1565G>T|||||1565|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2849G>T|||||2849|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1325G>T|||||1325|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*489G>T|||||489|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*237G>T|||||237|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:26,2:26:966:2:30:0,-5.57887,-84.3963

-NC_045512.2	26713	.	GTTTTGTGC	GTTTGTGC	52.4197	.	AB=0.214286;ABP=22.8638;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1M1D7M;DP=28;DPB=27.3333;DPRA=0;EPP=16.0391;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=12.0701;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=233;QR=834;RO=22;RPL=3;RPP=3.0103;RPPR=3.0103;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=11;SRP=3.0103;SRR=11;TYPE=del;ANN=GTTTGTGC|frameshift_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.195delT|p.Phe65fs|195/669|195/669|65/222||,GTTTGTGC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-485delT|||||485|,GTTTGTGC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-677delT|||||677|,GTTTGTGC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1039delT|||||1039|,GTTTGTGC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1177delT|||||1177|,GTTTGTGC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1557delT|||||1557|,GTTTGTGC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2841delT|||||2841|,GTTTGTGC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1333delT|||||1333|,GTTTGTGC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*497delT|||||497|,GTTTGTGC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*245delT|||||245|;LOF=(M|GU280_gp05|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:28:22,6:22:834:6:233:-12.9112,0,-66.9546

-NC_045512.2	26801	.	C	G	364.824	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=14;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=33.4109;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=24.0133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=542;QR=0;RO=0;RPL=14;RPP=33.4109;RPPR=0;RPR=0;RUN=1;SAF=0;SAP=33.4109;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.279C>G|p.Leu93Leu|279/669|279/669|93/222||,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-401C>G|||||401|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-593C>G|||||593|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-955C>G|||||955|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1093C>G|||||1093|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1473C>G|||||1473|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2757C>G|||||2757|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1417C>G|||||1417|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*581C>G|||||581|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*329C>G|||||329|	GT:DP:AD:RO:QR:AO:QA:GL	1/1:14:0,14:0:0:14:542:-49.1257,-4.21442,0

-NC_045512.2	26907	.	CTG	CG	4.02707E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=16;DPB=15.6667;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.4962;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=538;RO=15;RPL=1;RPP=5.18177;RPPR=6.62942;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=6.62942;SRR=10;TYPE=del;ANN=CG|frameshift_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.386delT|p.Leu129fs|386/669|386/669|129/222||,CG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-294delT|||||294|,CG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-486delT|||||486|,CG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-848delT|||||848|,CG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-986delT|||||986|,CG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1366delT|||||1366|,CG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2650delT|||||2650|,CG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1524delT|||||1524|,CG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*688delT|||||688|,CG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*436delT|||||436|;LOF=(M|GU280_gp05|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:538:1:33:0,-1.51734,-45.4542

-NC_045512.2	26983	.	A	T	1.30042E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.0214;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=340;RO=9;RPL=0;RPP=5.18177;RPPR=3.25157;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.461A>T|p.His154Leu|461/669|461/669|154/222||,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-219A>T|||||219|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-411A>T|||||411|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-773A>T|||||773|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-911A>T|||||911|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1291A>T|||||1291|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2575A>T|||||2575|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1599A>T|||||1599|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*763A>T|||||763|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*511A>T|||||511|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:340:1:14:0,-1.61031,-29.5553

-NC_045512.2	27151	.	ATTCC	ATCC	3.05576E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=28;DPB=27.8;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.6541;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=996;RO=27;RPL=0;RPP=5.18177;RPPR=26.2531;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=22;SRP=26.2531;SRR=5;TYPE=del;ANN=ATCC|frameshift_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.631delT|p.Ser211fs|631/669|631/669|211/222||,ATCC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-49delT|||||49|,ATCC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-241delT|||||241|,ATCC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-603delT|||||603|,ATCC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-741delT|||||741|,ATCC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1121delT|||||1121|,ATCC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2405delT|||||2405|,ATCC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1769delT|||||1769|,ATCC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*933delT|||||933|,ATCC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*681delT|||||681|;LOF=(M|GU280_gp05|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:996:1:37:0,-4.73101,-86.2575

-NC_045512.2	27166	.	ACA	AA	3.25162E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=29;DPB=28.6667;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.5477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1076;RO=28;RPL=0;RPP=5.18177;RPPR=28.1373;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=23;SRP=28.1373;SRR=5;TYPE=del;ANN=AA|frameshift_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.645delC|p.Asp215fs|645/669|645/669|215/222||,AA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-35delC|||||35|,AA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-227delC|||||227|,AA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-589delC|||||589|,AA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-727delC|||||727|,AA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1107delC|||||1107|,AA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2391delC|||||2391|,AA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1783delC|||||1783|,AA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*947delC|||||947|,AA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*695delC|||||695|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:29:28,1:28:1076:1:39:0,-4.83331,-93.2509

-NC_045512.2	27207	.	T	A	2.75888E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=35.6719;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=40;QR=1127;RO=29;RPL=0;RPP=5.18177;RPPR=30.0414;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=30.0414;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.6T>A|p.Phe2Leu|6/186|6/186|2/61||,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-187T>A|||||187|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-549T>A|||||549|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-687T>A|||||687|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1067T>A|||||1067|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2351T>A|||||2351|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1823T>A|||||1823|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*987T>A|||||987|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*735T>A|||||735|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*16T>A|||||16|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1127:1:40:0,-5.03522,-97.7335

-NC_045512.2	27211	.	CTC	CC	2.74836E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=30;DPB=29.6667;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.2757;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=1098;RO=29;RPL=1;RPP=5.18177;RPPR=36.0317;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=36.0317;SRR=4;TYPE=del;ANN=CC|frameshift_variant|HIGH|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.11delT|p.Leu4fs|11/186|11/186|4/61||,CC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-182delT|||||182|,CC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-544delT|||||544|,CC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-682delT|||||682|,CC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1062delT|||||1062|,CC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2346delT|||||2346|,CC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1828delT|||||1828|,CC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*992delT|||||992|,CC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*740delT|||||740|,CC|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*21delT|||||21|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1098:1:33:0,-5.73176,-95.8221

-NC_045512.2	27427	.	C	T	2.10949E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=48.9587;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.52;NS=1;NUMALT=1;ODDS=36.2466;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=938;RO=25;RPL=1;RPP=5.18177;RPPR=57.2971;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=48.9587;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.34C>T|p.Leu12Phe|34/366|34/366|12/121||,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-329C>T|||||329|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-467C>T|||||467|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-847C>T|||||847|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2131C>T|||||2131|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2043C>T|||||2043|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1207C>T|||||1207|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*955C>T|||||955|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*236C>T|||||236|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*40C>T|||||40|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:938:1:14:0,-6.42679,-83.3019

-NC_045512.2	27531	.	T	C	9.40218E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.2535;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=605;RO=18;RPL=1;RPP=5.18177;RPPR=20.3821;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=3;SRP=20.3821;SRR=15;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.138T>C|p.Phe46Phe|138/366|138/366|46/121||,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-225T>C|||||225|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-363T>C|||||363|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-743T>C|||||743|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2027T>C|||||2027|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2147T>C|||||2147|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1311T>C|||||1311|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1059T>C|||||1059|,C|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*340T>C|||||340|,C|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*144T>C|||||144|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:605:1:34:0,-2.32066,-51.3648

-NC_045512.2	27619	.	CAGT	CT	15.8571	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M2D1M;DP=6;DPB=5;DPRA=0;EPP=7.35324;EPPR=11.6962;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.62493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=154;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.0103;SRR=2;TYPE=del;ANN=CT|frameshift_variant|HIGH|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.227_228delAG|p.Gln76fs|227/366|227/366|76/121||,CT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-136_-135delAG|||||136|,CT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-274_-273delAG|||||274|,CT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-654_-653delAG|||||654|,CT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1938_-1937delAG|||||1938|,CT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2236_*2237delAG|||||2236|,CT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1400_*1401delAG|||||1400|,CT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1148_*1149delAG|||||1148|,CT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*429_*430delAG|||||429|,CT|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*233_*234delAG|||||233|;LOF=(ORF7a|GU280_gp07|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6:4,2:4:154:2:76:-5.40849,0,-12.4274

-NC_045512.2	27744	.	A	G	1.65615	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.772712;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=78;RO=2;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.351A>G|p.Lys117Lys|351/366|351/366|117/121||,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-12A>G|||||12|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-150A>G|||||150|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-530A>G|||||530|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1814A>G|||||1814|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2360A>G|||||2360|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1524A>G|||||1524|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1272A>G|||||1272|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*553A>G|||||553|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*357A>G|||||357|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:78:1:39:-2.99347,0,-6.50038

-NC_045512.2	27769	.	C	T	1.65794	.	AB=0.333333;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.772712;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=77;RO=2;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.14C>T|p.Ser5Leu|14/132|14/132|5/43||,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-125C>T|||||125|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-505C>T|||||505|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1789C>T|||||1789|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2385C>T|||||2385|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1549C>T|||||1549|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1297C>T|||||1297|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*578C>T|||||578|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*382C>T|||||382|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*10C>T|||||10|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3:2,1:2:77:1:39:-2.99347,0,-6.40605

-NC_045512.2	27789	.	TGCTTTTTAG	TGCTTTTAG,TGGCTTTTTAG	1.61783E-9	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=3M1D6M,1M1I9M;DP=20;DPB=20;DPRA=0,0;EPP=5.18177,5.18177;EPPR=42.0968;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=21.936;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=39,33;QR=645;RO=18;RPL=1,0;RPP=5.18177,5.18177;RPPR=26.6552;RPR=0,1;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=16;SRP=26.6552;SRR=2;TYPE=del,ins;ANN=TGGCTTTTTAG|frameshift_variant|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.35dupG|p.Cys12fs|36/132|36/132|12/43||,TGCTTTTAG|frameshift_variant|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.41delT|p.Leu14fs|41/132|41/132|14/43||,TGGCTTTTTAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-104dupG|||||103|,TGCTTTTAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-98delT|||||98|,TGGCTTTTTAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-484dupG|||||483|,TGCTTTTAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-478delT|||||478|,TGGCTTTTTAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1768dupG|||||1767|,TGCTTTTAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1762delT|||||1762|,TGGCTTTTTAG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2406dupG|||||2407|,TGCTTTTAG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2412delT|||||2412|,TGGCTTTTTAG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1570dupG|||||1571|,TGCTTTTAG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1576delT|||||1576|,TGGCTTTTTAG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1318dupG|||||1319|,TGCTTTTAG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1324delT|||||1324|,TGGCTTTTTAG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*599dupG|||||600|,TGCTTTTAG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*605delT|||||605|,TGGCTTTTTAG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*403dupG|||||404|,TGCTTTTAG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*409delT|||||409|,TGGCTTTTTAG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*31dupG|||||32|,TGCTTTTAG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*37delT|||||37|;LOF=(ORF7b|GU280_gp08|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:18,1,1:18:645:1,1:39,33:0,-2.18279,-54.512,-2.78022,-52.1464,-55.0529

-NC_045512.2	27799	.	C	T	4.25981E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.3485;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=793;RO=21;RPL=0;RPP=5.18177;RPPR=26.2761;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=26.2761;SRR=3;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.44C>T|p.Ala15Val|44/132|44/132|15/43||,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-95C>T|||||95|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-475C>T|||||475|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1759C>T|||||1759|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2415C>T|||||2415|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1579C>T|||||1579|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1327C>T|||||1327|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*608C>T|||||608|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*412C>T|||||412|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*40C>T|||||40|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:793:1:38:0,-2.82539,-67.9006

-NC_045512.2	27916	.	G	C	1.99651E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=43.4331;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.1346;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=954;RO=26;RPL=1;RPP=5.18177;RPPR=8.35546;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=15.0369;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.23G>C|p.Gly8Ala|23/366|23/366|8/121||,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-358G>C|||||358|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1642G>C|||||1642|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2532G>C|||||2532|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1696G>C|||||1696|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1444G>C|||||1444|,C|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*725G>C|||||725|,C|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*529G>C|||||529|,C|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*157G>C|||||157|,C|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*29G>C|||||29|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:954:1:16:0,-6.52783,-84.5583

-NC_045512.2	27944	.	C	T	1207.32	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=38;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=77.0689;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=57.2844;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1468;QR=0;RO=0;RPL=19;RPP=3.0103;RPPR=0;RPR=19;RUN=1;SAF=20;SAP=3.23888;SAR=18;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.51C>T|p.His17His|51/366|51/366|17/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-330C>T|||||330|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1614C>T|||||1614|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2560C>T|||||2560|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1724C>T|||||1724|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1472C>T|||||1472|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*753C>T|||||753|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*557C>T|||||557|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*185C>T|||||185|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*57C>T|||||57|	GT:DP:AD:RO:QR:AO:QA:GL	1/1:38:0,38:0:0:38:1468:-132.395,-11.4391,0

-NC_045512.2	27990	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.0421;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1409;RO=37;RPL=0;RPP=5.18177;RPPR=3.5385;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.5385;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.97G>A|p.Val33Ile|97/366|97/366|33/121||,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-284G>A|||||284|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1568G>A|||||1568|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2606G>A|||||2606|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1770G>A|||||1770|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1518G>A|||||1518|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*799G>A|||||799|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*603G>A|||||603|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*231G>A|||||231|,A|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*103G>A|||||103|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1409:1:16:0,-9.83916,-125.485

-NC_045512.2	28003	.	G	T	2.10643E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=7.35324;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.4545;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=1333;RO=36;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.110G>T|p.Cys37Phe|110/366|110/366|37/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-271G>T|||||271|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1555G>T|||||1555|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2619G>T|||||2619|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1783G>T|||||1783|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1531G>T|||||1531|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*812G>T|||||812|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*616G>T|||||616|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*244G>T|||||244|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*116G>T|||||116|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:36,2:36:1333:2:78:0,-4.03567,-112.856

-NC_045512.2	28006	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.2724;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1432;RO=37;RPL=1;RPP=5.18177;RPPR=3.06899;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.113C>T|p.Pro38Leu|113/366|113/366|38/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-268C>T|||||268|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1552C>T|||||1552|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2622C>T|||||2622|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1786C>T|||||1786|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1534C>T|||||1534|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*815C>T|||||815|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*619C>T|||||619|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*247C>T|||||247|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*119C>T|||||119|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1432:1:15:0,-9.93915,-127.659

-NC_045512.2	28016	.	C	A	3.03012E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=7.35324;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.6717;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=1372;RO=36;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=19;SRP=3.25157;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.123C>A|p.Phe41Leu|123/366|123/366|41/121||,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-258C>A|||||258|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1542C>A|||||1542|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2632C>A|||||2632|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1796C>A|||||1796|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1544C>A|||||1544|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*825C>A|||||825|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*629C>A|||||629|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*257C>A|||||257|,A|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*129C>A|||||129|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:36,2:36:1372:2:77:0,-4.13,-116.448

-NC_045512.2	28046	.	TAGA	TA	2.95717E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M2D1M;DP=19;DPB=18.5;DPRA=0;EPP=5.18177;EPPR=26.6552;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.1076;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=691;RO=18;RPL=1;RPP=5.18177;RPPR=33.8935;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=33.8935;SRR=17;TYPE=del;ANN=TA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.155_156delGA|p.Arg52fs|155/366|155/366|52/121||,TA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-226_-225delGA|||||226|,TA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1510_-1509delGA|||||1510|,TA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2664_*2665delGA|||||2664|,TA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1828_*1829delGA|||||1828|,TA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1576_*1577delGA|||||1576|,TA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*857_*858delGA|||||857|,TA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*661_*662delGA|||||661|,TA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*289_*290delGA|||||289|,TA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*161_*162delGA|||||161|;LOF=(ORF8|GU280_gp09|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:691:1:39:0,-1.82301,-58.6262

-NC_045512.2	28056	.	GCACCTTTAATTGA	GTTCCTGTTTACCTTTTACAATTAATTGA,GTTCCTGTTTACCTTTTACAATTA	0.015325	.	AB=0.157895,0.0526316;ABP=22.325,36.0395;AC=1,0;AF=0.5,0;AN=2;AO=3,1;CIGAR=1M2X3M15I8M,1M8I1X6M3I4M1D1M;DP=19;DPB=22.9286;DPRA=0,0;EPP=9.52472,5.18177;EPPR=27.4756;GTI=0;LEN=29,24;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=5.64506;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=113,35;QR=570;RO=15;RPL=3,1;RPP=9.52472,5.18177;RPPR=35.5824;RPR=0,0;RUN=1,1;SAF=0,0;SAP=9.52472,5.18177;SAR=3,1;SRF=1;SRP=27.4756;SRR=14;TYPE=complex,complex;ANN=TTCCTGTTTACCTTTTACAATTA|frameshift_variant&missense_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.164_175delCACCTTTAATTGinsTTCCTGTTTACCTTTTACAATT|p.Ala55fs|164/366|164/366|55/121||INFO_REALIGN_3_PRIME,TTCCTGTTTACCTTTTACAATTAATTGA|missense_variant&conservative_inframe_insertion|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.164_168delCACCTinsTTCCTGTTTACCTTTTACAA|p.Ala55_Pro56delinsValProValTyrLeuLeuGln|164/366|164/366|55/121||INFO_REALIGN_3_PRIME,TTCCTGTTTACCTTTTACAATTA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-217_-205delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||217|,TTCCTGTTTACCTTTTACAATTAATTGA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-217_-205delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||217|,TTCCTGTTTACCTTTTACAATTA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1501_-1489delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||1501|,TTCCTGTTTACCTTTTACAATTAATTGA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1501_-1489delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||1501|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2673_*2685delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||2673|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2673_*2685delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||2673|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1837_*1849delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||1837|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1837_*1849delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||1837|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1585_*1597delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||1585|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1585_*1597delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||1585|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*866_*878delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||866|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*866_*878delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||866|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*670_*682delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||670|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*670_*682delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||670|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*298_*310delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||298|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*298_*310delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||298|,TTCCTGTTTACCTTTTACAATTA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*170_*182delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTA|||||170|,TTCCTGTTTACCTTTTACAATTAATTGA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*170_*182delCACCTTTAATTGAinsTTCCTGTTTACCTTTTACAATTAATTGA|||||170|;LOF=(ORF8|GU280_gp09|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:19:15,3,1:15:570:3,1:113,35:-4.7645,0,-45.8721,-6.43885,-43.9293,-52.8878

-NC_045512.2	28080	.	G	T	2.95717E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.1076;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=677;RO=18;RPL=1;RPP=5.18177;RPPR=42.0968;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=33.8935;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.187G>T|p.Asp63Tyr|187/366|187/366|63/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-194G>T|||||194|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1478G>T|||||1478|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2696G>T|||||2696|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1860G>T|||||1860|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1608G>T|||||1608|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*889G>T|||||889|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*693G>T|||||693|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*321G>T|||||321|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*193G>T|||||193|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:677:1:39:0,-1.82301,-57.3579

-NC_045512.2	28097	.	A	T	1.0698E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=90.0666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.4259;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1680;RO=44;RPL=0;RPP=5.18177;RPPR=4.78696;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=6.16881;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.204A>T|p.Lys68Asn|204/366|204/366|68/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-177A>T|||||177|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1461A>T|||||1461|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2713A>T|||||2713|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1877A>T|||||1877|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1625A>T|||||1625|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*906A>T|||||906|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*710A>T|||||710|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*338A>T|||||338|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*210A>T|||||210|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1680:1:21:0,-11.4464,-149.367

-NC_045512.2	28209	.	G	T	145.214	.	AB=0.243902;ABP=26.3669;AC=1;AF=0.5;AN=2;AO=10;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.0103;EPPR=4.76149;GTI=0;LEN=1;MEANALT=1;MQM=58.8;MQMR=60;NS=1;NUMALT=1;ODDS=33.4367;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=386;QR=1199;RO=31;RPL=3;RPP=6.48466;RPPR=4.76149;RPR=7;RUN=1;SAF=8;SAP=10.8276;SAR=2;SRF=26;SRP=33.9012;SRR=5;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.316G>T|p.Glu106*|316/366|316/366|106/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-65G>T|||||65|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1349G>T|||||1349|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2825G>T|||||2825|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1989G>T|||||1989|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1737G>T|||||1737|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1018G>T|||||1018|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*822G>T|||||822|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*450G>T|||||450|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*322G>T|||||322|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:31,10:31:1199:10:386:-22.7111,0,-95.8641

-NC_045512.2	28214	.	CTTTTTAG	CTTTTAG	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D6M;DP=50;DPB=49.875;DPRA=0;EPP=5.18177;EPPR=45.5977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7551;NS=1;NUMALT=1;ODDS=63.1151;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1871;RO=49;RPL=1;RPP=5.18177;RPPR=3.05462;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=15.8176;SRR=16;TYPE=del;ANN=CTTTTAG|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.326delT|p.Leu109fs|326/366|326/366|109/121||,CTTTTAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-55delT|||||55|,CTTTTAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1339delT|||||1339|,CTTTTAG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2835delT|||||2835|,CTTTTAG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1999delT|||||1999|,CTTTTAG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1747delT|||||1747|,CTTTTAG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1028delT|||||1028|,CTTTTAG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*832delT|||||832|,CTTTTAG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*460delT|||||460|,CTTTTAG|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*332delT|||||332|;LOF=(ORF8|GU280_gp09|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:50:49,1:49:1871:1:39:0,-11.1549,-164.703

-NC_045512.2	28401	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7273;NS=1;NUMALT=1;ODDS=62.4981;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1657;RO=44;RPL=1;RPP=5.18177;RPPR=31.4368;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=31.4368;SRR=34;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.128A>G|p.Gln43Arg|128/1260|128/1260|43/419||,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1157A>G|||||1157|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3017A>G|||||3017|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2181A>G|||||2181|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1929A>G|||||1929|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1210A>G|||||1210|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1014A>G|||||1014|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*642A>G|||||642|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*514A>G|||||514|,G|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*142A>G|||||142|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1657:1:12:0,-12.3464,-148.151

-NC_045512.2	28429	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=43;DPB=43;DPRA=0;EPP=5.18177;EPPR=94.2121;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7143;NS=1;NUMALT=1;ODDS=53.5619;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1628;RO=42;RPL=0;RPP=5.18177;RPPR=32.7905;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=32.7905;SRR=33;TYPE=snp;ANN=A|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.156G>A|p.Trp52*|156/1260|156/1260|52/419||,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1129G>A|||||1129|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3045G>A|||||3045|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2209G>A|||||2209|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1957G>A|||||1957|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1238G>A|||||1238|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1042G>A|||||1042|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*670G>A|||||670|,A|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*542G>A|||||542|,A|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*170G>A|||||170|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:43:42,1:42:1628:1:39:0,-9.04772,-142.852

-NC_045512.2	28456	.	GGAA	GA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M2D1M;DP=40;DPB=39.5;DPRA=0;EPP=5.18177;EPPR=71.2168;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=59.6923;NS=1;NUMALT=1;ODDS=51.0808;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1431;RO=39;RPL=1;RPP=5.18177;RPPR=15.538;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=23.1103;SRR=29;TYPE=del;ANN=GA|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.184_185delGA|p.Glu62fs|184/1260|184/1260|62/419||,GA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1101_-1100delGA|||||1101|,GA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3073_*3074delGA|||||3073|,GA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2237_*2238delGA|||||2237|,GA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1985_*1986delGA|||||1985|,GA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1266_*1267delGA|||||1266|,GA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1070_*1071delGA|||||1070|,GA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*698_*699delGA|||||698|,GA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*570_*571delGA|||||570|,GA|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*198_*199delGA|||||198|;LOF=(N|GU280_gp10|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1431:1:32:0,-8.84189,-125.856

-NC_045512.2	28647	.	C	T	3.05998E-5	.	AB=0.0833333;ABP=21.1059;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=7.94546;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.8631;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=429;RO=11;RPL=0;RPP=5.18177;RPPR=7.94546;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=26.8965;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.374C>T|p.Ala125Val|374/1260|374/1260|125/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-911C>T|||||911|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3263C>T|||||3263|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2427C>T|||||2427|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2175C>T|||||2175|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1456C>T|||||1456|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1260C>T|||||1260|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*888C>T|||||888|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*760C>T|||||760|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*388C>T|||||388|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:12:11,1:11:429:1:39:-0.284205,0,-35.3533

-NC_045512.2	28719	.	GCAATC	GC	3.36816E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M4D1M;DP=17;DPB=16.3333;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.6749;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=610;RO=16;RPL=1;RPP=5.18177;RPPR=3.55317;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.55317;SRR=9;TYPE=del;ANN=GC|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.448_451delAATC|p.Asn150fs|448/1260|448/1260|150/419||,GC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-837_-834delAATC|||||837|,GC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3337_*3340delAATC|||||3337|,GC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2501_*2504delAATC|||||2501|,GC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2249_*2252delAATC|||||2249|,GC|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1530_*1533delAATC|||||1530|,GC|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1334_*1337delAATC|||||1334|,GC|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*962_*965delAATC|||||962|,GC|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*834_*837delAATC|||||834|,GC|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*462_*465delAATC|||||462|;LOF=(N|GU280_gp10|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:610:1:38:0,-1.32024,-51.4431

-NC_045512.2	28762	.	A	G	4.23339E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.4462;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=613;RO=16;RPL=0;RPP=5.18177;RPPR=5.18177;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=6;SRP=5.18177;SRR=10;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.489A>G|p.Gln163Gln|489/1260|489/1260|163/419||,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-796A>G|||||796|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3378A>G|||||3378|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2542A>G|||||2542|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2290A>G|||||2290|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1571A>G|||||1571|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1375A>G|||||1375|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1003A>G|||||1003|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*875A>G|||||875|,G|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*503A>G|||||503|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:613:1:39:0,-1.22095,-51.6136

-NC_045512.2	28849	.	C	T	46.5729	.	AB=0.285714;ABP=8.59409;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=11.6962;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.7238;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=385;RO=10;RPL=2;RPP=3.0103;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.576C>T|p.Asn192Asn|576/1260|576/1260|192/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-709C>T|||||709|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3465C>T|||||3465|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2629C>T|||||2629|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2377C>T|||||2377|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1658C>T|||||1658|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1462C>T|||||1462|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1090C>T|||||1090|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*962C>T|||||962|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*590C>T|||||590|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:14:10,4:10:385:4:153:-9.92732,0,-30.7925

-NC_045512.2	28881	.	GGG	AAC	45.6544	.	AB=0.285714;ABP=8.59409;AC=1;AF=0.5;AN=2;AO=4;CIGAR=3X;DP=14;DPB=14;DPRA=0;EPP=11.6962;EPPR=24.725;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.5123;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=152;QR=384;RO=10;RPL=2;RPP=3.0103;RPPR=3.0103;RPR=2;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=5;SRP=3.0103;SRR=5;TYPE=complex;ANN=AAC|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608_610delGGGinsAAC|p.ArgGly203LysArg|608/1260|608/1260|203/419||,AAC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-677_-675delGGGinsAAC|||||677|,AAC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3497_*3499delGGGinsAAC|||||3497|,AAC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2661_*2663delGGGinsAAC|||||2661|,AAC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2409_*2411delGGGinsAAC|||||2409|,AAC|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1690_*1692delGGGinsAAC|||||1690|,AAC|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1494_*1496delGGGinsAAC|||||1494|,AAC|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1122_*1124delGGGinsAAC|||||1122|,AAC|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*994_*996delGGGinsAAC|||||994|,AAC|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*622_*624delGGGinsAAC|||||622|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:14:10,4:10:384:4:152:-9.83547,0,-30.7022

-NC_045512.2	28918	.	T	G	1.66668E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.3784;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=385;RO=12;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=5;SRP=3.73412;SRR=7;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.645T>G|p.Gly215Gly|645/1260|645/1260|215/419||,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-640T>G|||||640|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3534T>G|||||3534|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2698T>G|||||2698|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2446T>G|||||2446|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1727T>G|||||1727|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1531T>G|||||1531|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1159T>G|||||1159|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1031T>G|||||1031|,G|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*659T>G|||||659|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:385:1:12:0,-2.7134,-33.7477

-NC_045512.2	28932	.	C	T	85.0336	.	AB=0.714286;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=13.8677;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.62353;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=194;QR=78;RO=2;RPL=0;RPP=13.8677;RPPR=7.35324;RPR=5;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.659C>T|p.Ala220Val|659/1260|659/1260|220/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-626C>T|||||626|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3548C>T|||||3548|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2712C>T|||||2712|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2460C>T|||||2460|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1741C>T|||||1741|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1545C>T|||||1545|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1173C>T|||||1173|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1045C>T|||||1045|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*673C>T|||||673|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:2,5:2:78:5:194:-15.7256,0,-5.29626

-NC_045512.2	29049	.	G	A	0.00330346	.	AB=0.125;ABP=12.7819;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.18177;EPPR=18.2106;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=7.18096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=265;RO=7;RPL=1;RPP=5.18177;RPPR=10.7656;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=1;SRP=10.7656;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.776G>A|p.Arg259Gln|776/1260|776/1260|259/419||,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-509G>A|||||509|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3665G>A|||||3665|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2829G>A|||||2829|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2577G>A|||||2577|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1858G>A|||||1858|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1662G>A|||||1662|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1290G>A|||||1290|,A|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1162G>A|||||1162|,A|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*790G>A|||||790|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:8:7,1:7:265:1:37:-1.28959,0,-21.8034

-NC_045512.2	29645	.	G	T	495.037	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=15;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=14.7363;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=25.3996;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=585;QR=0;RO=0;RPL=9;RPP=4.31318;RPPR=0;RPR=6;RUN=1;SAF=6;SAP=4.31318;SAR=9;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding|1/1|c.88G>T|p.Val30Leu|88/117|88/117|30/38||,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4261G>T|||||4261|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*3425G>T|||||3425|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*3173G>T|||||3173|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*2454G>T|||||2454|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*2258G>T|||||2258|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1886G>T|||||1886|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1758G>T|||||1758|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*1386G>T|||||1386|,T|downstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.*112G>T|||||112|	GT:DP:AD:RO:QR:AO:QA:GL	1/1:15:0,15:0:0:15:585:-52.9933,-4.51545,0

-NC_045512.2	29692	.	G	T	7.09404E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=23.2217;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.6274;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=503;RO=13;RPL=1;RPP=5.18177;RPPR=3.17734;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=6;SRP=3.17734;SRR=7;TYPE=snp;ANN=T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4308G>T|||||4308|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*3472G>T|||||3472|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*3220G>T|||||3220|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*2501G>T|||||2501|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*2305G>T|||||2305|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1933G>T|||||1933|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1805G>T|||||1805|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*1433G>T|||||1433|,T|downstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.*159G>T|||||159|,T|downstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.*18G>T|||||18|,T|intergenic_region|MODIFIER|ORF10-CHR_END|GU280_gp11-CHR_END|intergenic_region|GU280_gp11-CHR_END|||n.29692G>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:503:1:34:0,-0.815509,-42.2193

+NC_045512.2	32	.	C	A	3.56727E-5	.	AB=0.0909091;ABP=19.0002;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=5.18177;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7097;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=340;RO=10;RPL=0;RPP=5.18177;RPPR=24.725;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=24.725;SRR=0;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-234C>A|||||234|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-234C>A|||||234|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-234C>A|||||234|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-234C>A|||||234|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-774C>A|||||774|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-774C>A|||||774|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2688C>A|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2688C>A|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.32C>A||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:10,1:10:340:1:34:-0.0875811,0,-27.6188

+NC_045512.2	117	.	C	A	2.06691E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.3774;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=19;QR=707;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.44459;SRR=9;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-149C>A|||||149|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-149C>A|||||149|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-149C>A|||||149|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-149C>A|||||149|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-689C>A|||||689|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-689C>A|||||689|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2603C>A|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2603C>A|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.117C>A||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:707:1:19:0,-4.42166,-62.044

+NC_045512.2	123	.	C	A	1.76706E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.9102;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=705;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.44459;SRR=9;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-143C>A|||||143|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-143C>A|||||143|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-143C>A|||||143|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-143C>A|||||143|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-683C>A|||||683|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-683C>A|||||683|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2597C>A|||||2597|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2597C>A|||||2597|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.123C>A||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:705:1:8:0,-5.52163,-62.9622

+NC_045512.2	161	.	A	T	2.12537E-6	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=3.12459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=718;RO=19;RPL=0;RPP=7.35324;RPPR=44.2683;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-105A>T|||||105|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-105A>T|||||105|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-105A>T|||||105|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-105A>T|||||105|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-645A>T|||||645|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-645A>T|||||645|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2559A>T|||||2559|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2559A>T|||||2559|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.161A>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:718:2:76:-0.893181,0,-58.6313

+NC_045512.2	204	.	G	T	2.12537E-6	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=7.35324;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=695;RO=19;RPL=1;RPP=3.0103;RPPR=3.12459;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.12459;SRR=9;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-62G>T|||||62|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-62G>T|||||62|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-62G>T|||||62|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-62G>T|||||62|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-602G>T|||||602|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-602G>T|||||602|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2516G>T|||||2516|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2516G>T|||||2516|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.204G>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:695:2:76:-0.893181,0,-56.5538

+NC_045512.2	241	.	C	T	616.567	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=21;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=48.6112;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=33.7174;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=769;QR=0;RO=0;RPL=11;RPP=3.1137;RPPR=0;RPR=10;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-25C>T|||||25|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-25C>T|||||25|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-25C>T|||||25|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-25C>T|||||25|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-565C>T|||||565|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-565C>T|||||565|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2479C>T|||||2479|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2479C>T|||||2479|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.241C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	1/1:21:0,21:0:0:21:769:-69.5268,-6.32163,0

+NC_045512.2	328	.	ACA	ACCA	9.67365E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=36;DPB=36.3333;DPRA=0;EPP=5.18177;EPPR=68.4099;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=43.4814;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1233;RO=34;RPL=0;RPP=5.18177;RPPR=12.2071;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=15.5282;SRR=10;TYPE=ins;ANN=ACCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.64dupC|p.Gln22fs|65/21291|65/21291|22/7096||,ACCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.64dupC|p.Gln22fs|65/540|65/540|22/179||WARNING_TRANSCRIPT_NO_STOP_CODON,ACCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.64dupC|p.Gln22fs|65/540|65/540|22/179||WARNING_TRANSCRIPT_NO_STOP_CODON,ACCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.64dupC|p.Gln22fs|65/13218|65/13218|22/4405||,ACCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-477dupC|||||476|WARNING_TRANSCRIPT_NO_START_CODON,ACCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-477dupC|||||476|WARNING_TRANSCRIPT_NO_START_CODON,ACCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2391dupC|||||2390|WARNING_TRANSCRIPT_NO_START_CODON,ACCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2391dupC|||||2390|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,1:34:1233:1:38:0,-6.98864,-107.578

+NC_045512.2	355	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7073;NS=1;NUMALT=1;ODDS=52.4278;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1555;RO=41;RPL=1;RPP=5.18177;RPPR=31.0276;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=31.0276;SRR=9;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.90C>T|p.Gly30Gly|90/21291|90/21291|30/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.90C>T|p.Gly30Gly|90/540|90/540|30/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.90C>T|p.Gly30Gly|90/540|90/540|30/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.90C>T|p.Gly30Gly|90/13218|90/13218|30/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-451C>T|||||451|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-451C>T|||||451|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2365C>T|||||2365|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2365C>T|||||2365|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1555:1:38:0,-8.84599,-136.397

+NC_045512.2	366	.	C	T	186.222	.	AB=0.333333;ABP=13.1438;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=33.4109;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=42.8793;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=528;QR=1064;RO=28;RPL=0;RPP=33.4109;RPPR=7.97367;RPR=14;RUN=1;SAF=14;SAP=33.4109;SAR=0;SRF=18;SRP=7.97367;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.101C>T|p.Ser34Phe|101/21291|101/21291|34/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.101C>T|p.Ser34Phe|101/540|101/540|34/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.101C>T|p.Ser34Phe|101/540|101/540|34/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.101C>T|p.Ser34Phe|101/13218|101/13218|34/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-440C>T|||||440|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-440C>T|||||440|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2354C>T|||||2354|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2354C>T|||||2354|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:42:28,14:28:1064:14:528:-35.1856,0,-83.4276

+NC_045512.2	401	.	CTTAA	CTAA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D3M;DP=37;DPB=36.6;DPRA=0;EPP=7.35324;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6571;NS=1;NUMALT=1;ODDS=40.215;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=1319;RO=35;RPL=2;RPP=7.35324;RPPR=55.1877;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=32;SRP=55.1877;SRR=3;TYPE=del;ANN=CTAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.138delT|p.Asp48fs|138/21291|138/21291|46/7096||,CTAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.138delT|p.Asp48fs|138/540|138/540|46/179||WARNING_TRANSCRIPT_NO_STOP_CODON,CTAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.138delT|p.Asp48fs|138/540|138/540|46/179||WARNING_TRANSCRIPT_NO_STOP_CODON,CTAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.138delT|p.Asp48fs|138/13218|138/13218|46/4405||,CTAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-403delT|||||403|WARNING_TRANSCRIPT_NO_START_CODON,CTAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-403delT|||||403|WARNING_TRANSCRIPT_NO_START_CODON,CTAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2317delT|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,CTAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2317delT|||||2317|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:35,2:35:1319:2:61:0,-5.34435,-113.176

+NC_045512.2	406	.	AGA	AA	1.27173E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=35;DPB=35.3333;DPRA=0;EPP=5.18177;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=44.6059;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=34;PRO=1;QA=34;QR=1277;RO=34;RPL=1;RPP=5.18177;RPPR=60.4905;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=60.4905;SRR=2;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.142delG|p.Asp48fs|142/21291|142/21291|48/7096||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.142delG|p.Asp48fs|142/540|142/540|48/179||WARNING_TRANSCRIPT_NO_STOP_CODON,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.142delG|p.Asp48fs|142/540|142/540|48/179||WARNING_TRANSCRIPT_NO_STOP_CODON,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.142delG|p.Asp48fs|142/13218|142/13218|48/4405||,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-399delG|||||399|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-399delG|||||399|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2313delG|||||2313|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2313delG|||||2313|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:34,1:34:1277:1:34:0,-7.47703,-111.792

+NC_045512.2	421	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=5.18177;EPPR=53.0819;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=42.906;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1265;RO=34;RPL=0;RPP=5.18177;RPPR=76.8404;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=53.0819;SRR=3;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.156C>A|p.Gly52Gly|156/21291|156/21291|52/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.156C>A|p.Gly52Gly|156/540|156/540|52/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.156C>A|p.Gly52Gly|156/540|156/540|52/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.156C>A|p.Gly52Gly|156/13218|156/13218|52/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-385C>A|||||385|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-385C>A|||||385|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2299C>A|||||2299|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2299C>A|||||2299|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:34,1:34:1265:1:38:0,-6.73878,-110.313

+NC_045512.2	442	.	C	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=89.6368;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2254;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.177C>G|p.Gly59Gly|177/21291|177/21291|59/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.177C>G|p.Gly59Gly|177/540|177/540|59/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.177C>G|p.Gly59Gly|177/540|177/540|59/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.177C>G|p.Gly59Gly|177/13218|177/13218|59/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-364C>G|||||364|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-364C>G|||||364|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2278C>G|||||2278|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2278C>G|||||2278|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:63,1:63:2254:1:7:0,-18.5659,-202.353

+NC_045512.2	445	.	T	C	647.516	.	AB=0.484375;ABP=3.14602;AC=1;AF=0.5;AN=2;AO=31;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.08035;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=59.2258;MQMR=60;NS=1;NUMALT=1;ODDS=149.096;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1087;QR=1196;RO=33;RPL=0;RPP=70.3259;RPPR=74.6689;RPR=31;RUN=1;SAF=16;SAP=3.08035;SAR=15;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.180T>C|p.Val60Val|180/21291|180/21291|60/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.180T>C|p.Val60Val|180/540|180/540|60/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.180T>C|p.Val60Val|180/540|180/540|60/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.180T>C|p.Val60Val|180/13218|180/13218|60/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-361T>C|||||361|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-361T>C|||||361|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2275T>C|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2275T>C|||||2275|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:64:33,31:33:1196:31:1087:-78.8078,0,-88.6688

+NC_045512.2	460	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=89.6368;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2266;RO=63;RPL=0;RPP=5.18177;RPPR=139.813;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.195A>C|p.Glu65Asp|195/21291|195/21291|65/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.195A>C|p.Glu65Asp|195/540|195/540|65/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.195A>C|p.Glu65Asp|195/540|195/540|65/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.195A>C|p.Glu65Asp|195/13218|195/13218|65/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-346A>C|||||346|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-346A>C|||||346|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2260A>C|||||2260|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2260A>C|||||2260|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:63,1:63:2266:1:7:0,-18.5659,-203.41

+NC_045512.2	505	.	T	A	1.73301E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=139.813;GTI=0;LEN=1;MEANALT=1;MQM=48;MQMR=59.8095;NS=1;NUMALT=1;ODDS=84.1303;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=2312;RO=63;RPL=1;RPP=5.18177;RPPR=3.04477;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.240T>A|p.Pro80Pro|240/21291|240/21291|80/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.240T>A|p.Pro80Pro|240/540|240/540|80/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.240T>A|p.Pro80Pro|240/540|240/540|80/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.240T>A|p.Pro80Pro|240/13218|240/13218|80/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-301T>A|||||301|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-301T>A|||||301|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2215T>A|||||2215|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2215T>A|||||2215|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:63,1:63:2312:1:31:0,-16.1745,-205.204

+NC_045512.2	541	.	CGA	CA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D1M;DP=64;DPB=63.3333;DPRA=0;EPP=7.35324;EPPR=137.642;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=71.879;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2328;RO=62;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=31;SRP=3.0103;SRR=31;TYPE=del;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.277delG|p.Glu93fs|277/21291|277/21291|93/7096||,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.277delG|p.Glu93fs|277/540|277/540|93/179||WARNING_TRANSCRIPT_NO_STOP_CODON,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.277delG|p.Glu93fs|277/540|277/540|93/179||WARNING_TRANSCRIPT_NO_STOP_CODON,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.277delG|p.Glu93fs|277/13218|277/13218|93/4405||,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-264delG|||||264|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-264delG|||||264|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2178delG|||||2178|WARNING_TRANSCRIPT_NO_START_CODON,CA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2178delG|||||2178|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:62,2:62:2328:2:76:0,-12.0511,-202.468

+NC_045512.2	560	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=7.35324;EPPR=137.642;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6129;NS=1;NUMALT=1;ODDS=71.879;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2315;RO=62;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=31;SRP=3.0103;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.295C>T|p.Arg99Cys|295/21291|295/21291|99/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.295C>T|p.Arg99Cys|295/540|295/540|99/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.295C>T|p.Arg99Cys|295/540|295/540|99/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.295C>T|p.Arg99Cys|295/13218|295/13218|99/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-246C>T|||||246|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-246C>T|||||246|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2160C>T|||||2160|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2160C>T|||||2160|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:62,2:62:2315:2:76:0,-12.0511,-201.298

+NC_045512.2	577	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.04477;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=89.1762;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2353;RO=63;RPL=1;RPP=5.18177;RPPR=131.265;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=31;SRP=3.04477;SRR=32;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.312T>G|p.Leu104Leu|312/21291|312/21291|104/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.312T>G|p.Leu104Leu|312/540|312/540|104/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.312T>G|p.Leu104Leu|312/540|312/540|104/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.312T>G|p.Leu104Leu|312/13218|312/13218|104/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-229T>G|||||229|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-229T>G|||||229|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2143T>G|||||2143|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2143T>G|||||2143|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:63,1:63:2353:1:9:0,-18.3659,-211.033

+NC_045512.2	578	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=5.18177;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.619;NS=1;NUMALT=1;ODDS=84.3418;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=2356;RO=63;RPL=1;RPP=5.18177;RPPR=131.265;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.313G>A|p.Gly105Ser|313/21291|313/21291|105/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.313G>A|p.Gly105Ser|313/540|313/540|105/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.313G>A|p.Gly105Ser|313/540|313/540|105/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.313G>A|p.Gly105Ser|313/13218|313/13218|105/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-228G>A|||||228|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-228G>A|||||228|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2142G>A|||||2142|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2142G>A|||||2142|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:64:63,1:63:2356:1:30:0,-16.2664,-209.204

+NC_045512.2	583	.	CC	TT,TC	601.468	.	AB=0.09375,0.4375;ABP=94.755,5.18177;AC=0,1;AF=0,0.5;AN=2;AO=6,28;CIGAR=2X,1X1M;DP=64;DPB=64;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.0103;GTI=0;LEN=2,1;MEANALT=2,2;MQM=60,59.1429;MQMR=60;NS=1;NUMALT=2;ODDS=138.493;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=218,1009;QR=1114;RO=30;RPL=6,28;RPP=16.0391,63.8115;RPPR=68.1545;RPR=0,0;RUN=1,1;SAF=3,14;SAP=3.0103,3.0103;SAR=3,14;SRF=15;SRP=3.0103;SRR=15;TYPE=complex,snp;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.318_319delCCinsTT|p.Leu107Phe|318/21291|318/21291|106/7096||,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.318_319delCCinsTT|p.Leu107Phe|318/540|318/540|106/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.318_319delCCinsTT|p.Leu107Phe|318/540|318/540|106/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.318_319delCCinsTT|p.Leu107Phe|318/13218|318/13218|106/4405||,TC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.318C>T|p.Val106Val|318/21291|318/21291|106/7096||,TC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.318C>T|p.Val106Val|318/540|318/540|106/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.318C>T|p.Val106Val|318/540|318/540|106/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.318C>T|p.Val106Val|318/13218|318/13218|106/4405||,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-223C>T|||||223|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-223_-222delCCinsTT|||||223|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-223C>T|||||223|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-223_-222delCCinsTT|||||223|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2137C>T|||||2137|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2137_-2136delCCinsTT|||||2137|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2137C>T|||||2137|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2137_-2136delCCinsTT|||||2137|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/2:64:30,6,28:30:1114:6,28:218,1009:-73.2231,-64.4502,-153.815,0,-73.3701,-82.7431

+NC_045512.2	593	.	C	T	610.965	.	AB=0.4375;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=28;CIGAR=1X;DP=64;DPB=64;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=140.68;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1038;QR=1263;RO=36;RPL=28;RPP=63.8115;RPPR=81.1833;RPR=0;RUN=1;SAF=14;SAP=3.0103;SAR=14;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.328C>T|p.His110Tyr|328/21291|328/21291|110/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.328C>T|p.His110Tyr|328/540|328/540|110/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.328C>T|p.His110Tyr|328/540|328/540|110/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.328C>T|p.His110Tyr|328/13218|328/13218|110/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-213C>T|||||213|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-213C>T|||||213|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2127C>T|||||2127|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2127C>T|||||2127|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:64:36,28:36:1263:28:1038:-74.3936,0,-94.685

+NC_045512.2	643	.	C	T	202.452	.	AB=0.358974;ABP=9.74743;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=33.4109;EPPR=57.2971;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=46.6162;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=532;QR=920;RO=25;RPL=14;RPP=33.4109;RPPR=13.5202;RPR=0;RUN=1;SAF=0;SAP=33.4109;SAR=14;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.378C>T|p.Asn126Asn|378/21291|378/21291|126/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.378C>T|p.Asn126Asn|378/540|378/540|126/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.378C>T|p.Asn126Asn|378/540|378/540|126/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.378C>T|p.Asn126Asn|378/13218|378/13218|126/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-163C>T|||||163|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-163C>T|||||163|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2077C>T|||||2077|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2077C>T|||||2077|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:39:25,14:25:920:14:532:-36.4501,0,-71.3774

+NC_045512.2	657	.	C	T	154.161	.	AB=0.28;ABP=24.0302;AC=1;AF=0.5;AN=2;AO=14;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=33.4109;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=59.1429;MQMR=60;NS=1;NUMALT=1;ODDS=35.4969;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=532;QR=1361;RO=36;RPL=14;RPP=33.4109;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=33.4109;SAR=14;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.392C>T|p.Ala131Val|392/21291|392/21291|131/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.392C>T|p.Ala131Val|392/540|392/540|131/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.392C>T|p.Ala131Val|392/540|392/540|131/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.392C>T|p.Ala131Val|392/13218|392/13218|131/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-149C>T|||||149|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-149C>T|||||149|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2063C>T|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2063C>T|||||2063|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:50:36,14:36:1361:14:532:-33.1387,0,-107.731

+NC_045512.2	663	.	G	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=105.24;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=66.0771;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1930;RO=51;RPL=1;RPP=5.18177;RPPR=8.16222;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=10.206;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.398G>C|p.Gly133Ala|398/21291|398/21291|133/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.398G>C|p.Gly133Ala|398/540|398/540|133/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.398G>C|p.Gly133Ala|398/540|398/540|133/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.398G>C|p.Gly133Ala|398/13218|398/13218|133/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-143G>C|||||143|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-143G>C|||||143|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2057G>C|||||2057|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2057G>C|||||2057|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:52:51,1:51:1930:1:38:0,-11.8563,-170.124

+NC_045512.2	666	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=5.18177;EPPR=105.24;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7647;NS=1;NUMALT=1;ODDS=66.0771;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1936;RO=51;RPL=0;RPP=5.18177;RPPR=10.206;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=12.5903;SRR=33;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.401A>T|p.His134Leu|401/21291|401/21291|134/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.401A>T|p.His134Leu|401/540|401/540|134/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.401A>T|p.His134Leu|401/540|401/540|134/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.401A>T|p.His134Leu|401/13218|401/13218|134/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-140A>T|||||140|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-140A>T|||||140|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2054A>T|||||2054|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2054A>T|||||2054|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:52:51,1:51:1936:1:38:0,-11.8563,-170.663

+NC_045512.2	682	.	T	C	342.715	.	AB=0.346154;ABP=13.7006;AC=1;AF=0.5;AN=2;AO=18;CIGAR=1X;DP=52;DPB=52;DPRA=0;EPP=33.8935;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.6471;NS=1;NUMALT=1;ODDS=78.913;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=665;QR=1292;RO=34;RPL=6;RPP=7.35324;RPPR=23.7032;RPR=12;RUN=1;SAF=11;SAP=4.9405;SAR=7;SRF=8;SRP=23.7032;SRR=26;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.417T>C|p.Asp139Asp|417/21291|417/21291|139/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.417T>C|p.Asp139Asp|417/540|417/540|139/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.417T>C|p.Asp139Asp|417/540|417/540|139/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.417T>C|p.Asp139Asp|417/13218|417/13218|139/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-124T>C|||||124|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-124T>C|||||124|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2038T>C|||||2038|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2038T>C|||||2038|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:52:34,18:34:1292:18:665:-44.5238,0,-100.888

+NC_045512.2	721	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=7.35324;EPPR=94.401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7391;NS=1;NUMALT=1;ODDS=59.7474;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1691;RO=46;RPL=2;RPP=7.35324;RPPR=4.70971;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=19;SRP=6.03148;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.456T>G|p.Asp152Glu|456/21291|456/21291|152/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.456T>G|p.Asp152Glu|456/540|456/540|152/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.456T>G|p.Asp152Glu|456/540|456/540|152/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.456T>G|p.Asp152Glu|456/13218|456/13218|152/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-85T>G|||||85|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-85T>G|||||85|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1999T>G|||||1999|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1999T>G|||||1999|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:46,2:46:1691:2:39:0,-10.7447,-148.746

+NC_045512.2	724	.	T	G	3.40528E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=83.5666;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.7073;NS=1;NUMALT=1;ODDS=54.0345;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1474;RO=41;RPL=1;RPP=5.18177;RPPR=3.06326;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.48696;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.459T>G|p.Pro153Pro|459/21291|459/21291|153/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.459T>G|p.Pro153Pro|459/540|459/540|153/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.459T>G|p.Pro153Pro|459/540|459/540|153/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.459T>G|p.Pro153Pro|459/13218|459/13218|153/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-82T>G|||||82|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-82T>G|||||82|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1996T>G|||||1996|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1996T>G|||||1996|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1474:1:31:0,-9.54381,-129.836

+NC_045512.2	725	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.3595;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=1335;RO=37;RPL=1;RPP=5.18177;RPPR=3.5385;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.460T>G|p.Tyr154Asp|460/21291|460/21291|154/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.460T>G|p.Tyr154Asp|460/540|460/540|154/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.460T>G|p.Tyr154Asp|460/540|460/540|154/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.460T>G|p.Tyr154Asp|460/13218|460/13218|154/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-81T>G|||||81|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-81T>G|||||81|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1995T>G|||||1995|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1995T>G|||||1995|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1335:1:32:0,-8.23983,-117.246

+NC_045512.2	729	.	A	G	2.90829E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1342;RO=36;RPL=0;RPP=5.18177;RPPR=81.1833;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.0103;SRR=18;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.464A>G|p.Glu155Gly|464/21291|464/21291|155/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.464A>G|p.Glu155Gly|464/540|464/540|155/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.464A>G|p.Glu155Gly|464/540|464/540|155/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.464A>G|p.Glu155Gly|464/13218|464/13218|155/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-77A>G|||||77|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-77A>G|||||77|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1991A>G|||||1991|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1991A>G|||||1991|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1342:1:38:0,-7.34084,-117.278

+NC_045512.2	737	.	C	A	3.28521E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.8841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1332;RO=37;RPL=0;RPP=5.18177;RPPR=83.3548;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=19;SRP=3.06899;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.472C>A|p.Gln158Lys|472/21291|472/21291|158/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.472C>A|p.Gln158Lys|472/540|472/540|158/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.472C>A|p.Gln158Lys|472/540|472/540|158/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.472C>A|p.Gln158Lys|472/13218|472/13218|158/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-69C>A|||||69|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-69C>A|||||69|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1983C>A|||||1983|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1983C>A|||||1983|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1332:1:8:0,-10.6391,-119.367

+NC_045512.2	913	.	C	T	595.642	.	AB=0.684211;ABP=14.2105;AC=1;AF=0.5;AN=2;AO=26;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.1502;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=935;QR=445;RO=12;RPL=26;RPP=59.4686;RPPR=29.068;RPR=0;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.648C>T|p.Ser216Ser|648/21291|648/21291|216/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.648C>T|p.Ser216Ser|648/13218|648/13218|216/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.108C>T|p.Ser36Ser|108/1914|108/1914|36/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.108C>T|p.Ser36Ser|108/1914|108/1914|36/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1807C>T|||||1807|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1807C>T|||||1807|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*108C>T|||||108|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*108C>T|||||108|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:38:12,26:12:445:26:935:-73.017,0,-28.9551

+NC_045512.2	924	.	A	T	3.28521E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.8841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1322;RO=37;RPL=1;RPP=5.18177;RPPR=83.3548;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.659A>T|p.Asp220Val|659/21291|659/21291|220/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.659A>T|p.Asp220Val|659/13218|659/13218|220/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.119A>T|p.Asp40Val|119/1914|119/1914|40/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.119A>T|p.Asp40Val|119/1914|119/1914|40/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1796A>T|||||1796|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1796A>T|||||1796|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*119A>T|||||119|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*119A>T|||||119|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1322:1:8:0,-10.6391,-118.459

+NC_045512.2	929	.	A	T	6.26083E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.6539;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1298;RO=37;RPL=1;RPP=5.18177;RPPR=83.3548;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.664A>T|p.Ile222Phe|664/21291|664/21291|222/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.664A>T|p.Ile222Phe|664/13218|664/13218|222/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.124A>T|p.Ile42Phe|124/1914|124/1914|42/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.124A>T|p.Ile42Phe|124/1914|124/1914|42/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1791A>T|||||1791|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1791A>T|||||1791|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*124A>T|||||124|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*124A>T|||||124|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1298:1:9:0,-10.5391,-116.202

+NC_045512.2	932	.	G	T	3.28521E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=3.06899;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=53.8841;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1322;RO=37;RPL=1;RPP=5.18177;RPPR=83.3548;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=18;SRP=3.06899;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.667G>T|p.Asp223Tyr|667/21291|667/21291|223/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.667G>T|p.Asp223Tyr|667/13218|667/13218|223/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.127G>T|p.Asp43Tyr|127/1914|127/1914|43/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.127G>T|p.Asp43Tyr|127/1914|127/1914|43/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1788G>T|||||1788|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1788G>T|||||1788|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*127G>T|||||127|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*127G>T|||||127|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1322:1:8:0,-10.6391,-118.464

+NC_045512.2	946	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=47.41;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.5293;PAIRED=1;PAIREDR=0.93617;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1674;RO=47;RPL=0;RPP=5.18177;RPPR=5.27418;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=28;SRP=6.75262;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.681T>G|p.Gly227Gly|681/21291|681/21291|227/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.681T>G|p.Gly227Gly|681/13218|681/13218|227/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.141T>G|p.Gly47Gly|141/1914|141/1914|47/637||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.141T>G|p.Gly47Gly|141/1914|141/1914|47/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1774T>G|||||1774|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1774T>G|||||1774|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*141T>G|||||141|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*141T>G|||||141|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:47,1:47:1674:1:34:0,-11.0505,-147.539

+NC_045512.2	949	.	A	G	1.43295E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=83.8559;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.3616;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1883;RO=52;RPL=0;RPP=5.18177;RPPR=4.51363;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=11.1951;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.684A>G|p.Val228Val|684/21291|684/21291|228/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.684A>G|p.Val228Val|684/13218|684/13218|228/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.144A>G|p.Val48Val|144/1914|144/1914|48/637||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.144A>G|p.Val48Val|144/1914|144/1914|48/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1771A>G|||||1771|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1771A>G|||||1771|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*144A>G|||||144|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*144A>G|||||144|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1883:1:34:0,-12.5557,-166.334

+NC_045512.2	954	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=107.408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.4248;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1958;RO=52;RPL=0;RPP=5.18177;RPPR=9.02361;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=11.1951;SRR=19;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.689G>T|p.Cys230Phe|689/21291|689/21291|230/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.689G>T|p.Cys230Phe|689/13218|689/13218|230/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.149G>T|p.Cys50Phe|149/1914|149/1914|50/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.149G>T|p.Cys50Phe|149/1914|149/1914|50/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1766G>T|||||1766|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1766G>T|||||1766|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*149G>T|||||149|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*149G>T|||||149|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1958:1:12:0,-14.7546,-175.276

+NC_045512.2	968	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1898;RO=50;RPL=1;RPP=5.18177;RPPR=14.1282;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=14.1282;SRR=17;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.703G>T|p.Glu235*|703/21291|703/21291|235/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.703G>T|p.Glu235*|703/13218|703/13218|235/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.163G>T|p.Glu55*|163/1914|163/1914|55/637||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.163G>T|p.Glu55*|163/1914|163/1914|55/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1752G>T|||||1752|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1752G>T|||||1752|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*163G>T|||||163|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*163G>T|||||163|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:51:50,1:50:1898:1:38:0,-11.5553,-167.28

+NC_045512.2	973	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1897;RO=50;RPL=0;RPP=5.18177;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.708T>A|p.His236Gln|708/21291|708/21291|236/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.708T>A|p.His236Gln|708/13218|708/13218|236/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.168T>A|p.His56Gln|168/1914|168/1914|56/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.168T>A|p.His56Gln|168/1914|168/1914|56/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1747T>A|||||1747|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1747T>A|||||1747|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*168T>A|||||168|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*168T>A|||||168|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:51:50,1:50:1897:1:38:0,-11.5553,-167.19

+NC_045512.2	998	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1892;RO=50;RPL=0;RPP=5.18177;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.733T>C|p.Ser245Pro|733/21291|733/21291|245/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.733T>C|p.Ser245Pro|733/13218|733/13218|245/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.193T>C|p.Ser65Pro|193/1914|193/1914|65/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.193T>C|p.Ser65Pro|193/1914|193/1914|65/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1722T>C|||||1722|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1722T>C|||||1722|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*193T>C|||||193|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*193T>C|||||193|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:51:50,1:50:1892:1:38:0,-11.5553,-166.741

+NC_045512.2	1019	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=51;DPB=51;DPRA=0;EPP=5.18177;EPPR=111.584;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.7103;PAIRED=1;PAIREDR=0.92;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1892;RO=50;RPL=0;RPP=5.18177;RPPR=11.5225;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=11.5225;SRR=18;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.754C>T|p.Gln252*|754/21291|754/21291|252/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.754C>T|p.Gln252*|754/13218|754/13218|252/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.214C>T|p.Gln72*|214/1914|214/1914|72/637||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.214C>T|p.Gln72*|214/1914|214/1914|72/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1701C>T|||||1701|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1701C>T|||||1701|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*214C>T|||||214|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*214C>T|||||214|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:51:50,1:50:1892:1:38:0,-11.5553,-166.741

+NC_045512.2	1026	.	C	T	6.48614E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=49;DPB=49;DPRA=0;EPP=5.18177;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.8949;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1730;RO=48;RPL=1;RPP=5.18177;RPPR=17.6677;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=17.6677;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.761C>T|p.Pro254Leu|761/21291|761/21291|254/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.761C>T|p.Pro254Leu|761/13218|761/13218|254/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.221C>T|p.Pro74Leu|221/1914|221/1914|74/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.221C>T|p.Pro74Leu|221/1914|221/1914|74/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1694C>T|||||1694|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1694C>T|||||1694|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*221C>T|||||221|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*221C>T|||||221|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:49:48,1:48:1730:1:34:0,-11.3516,-152.571

+NC_045512.2	1044	.	C	T	3.11712E-4	.	AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.54195;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=334;QR=2013;RO=56;RPL=0;RPP=22.5536;RPPR=124.613;RPR=9;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.779C>T|p.Ala260Val|779/21291|779/21291|260/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.779C>T|p.Ala260Val|779/13218|779/13218|260/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.239C>T|p.Ala80Val|239/1914|239/1914|80/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.239C>T|p.Ala80Val|239/1914|239/1914|80/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1676C>T|||||1676|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1676C>T|||||1676|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*239C>T|||||239|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*239C>T|||||239|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:65:56,9:56:2013:9:334:-10.8453,0,-161.85

+NC_045512.2	1069	.	G	A	8.67461E-8	.	AB=0.123077;ABP=83.2212;AC=1;AF=0.5;AN=2;AO=8;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.0103;EPPR=3.0484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.7288;PAIRED=1;PAIREDR=0.877193;PAO=0;PQA=0;PQR=0;PRO=0;QA=299;QR=2032;RO=57;RPL=0;RPP=20.3821;RPPR=126.784;RPR=8;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=29;SRP=3.0484;SRR=28;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.804G>A|p.Gly268Gly|804/21291|804/21291|268/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.804G>A|p.Gly268Gly|804/13218|804/13218|268/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.264G>A|p.Gly88Gly|264/1914|264/1914|88/637||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.264G>A|p.Gly88Gly|264/1914|264/1914|88/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1651G>A|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1651G>A|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*264G>A|||||264|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*264G>A|||||264|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:65:57,8:57:2032:8:299:-7.69887,0,-163.558

+NC_045512.2	1076	.	C	T	8.85674E-4	.	AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.49761;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=339;QR=2022;RO=56;RPL=0;RPP=22.5536;RPPR=124.613;RPR=9;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.811C>T|p.Pro271Ser|811/21291|811/21291|271/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.811C>T|p.Pro271Ser|811/13218|811/13218|271/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.271C>T|p.Pro91Ser|271/1914|271/1914|91/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.271C>T|p.Pro91Ser|271/1914|271/1914|91/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1644C>T|||||1644|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1644C>T|||||1644|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*271C>T|||||271|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*271C>T|||||271|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:65:56,9:56:2022:9:339:-11.2989,0,-162.66

+NC_045512.2	1126	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=141.985;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0865;PAIRED=1;PAIREDR=0.890625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2381;RO=64;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.861G>T|p.Arg287Ser|861/21291|861/21291|287/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.861G>T|p.Arg287Ser|861/13218|861/13218|287/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.321G>T|p.Arg107Ser|321/1914|321/1914|107/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.321G>T|p.Arg107Ser|321/1914|321/1914|107/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1594G>T|||||1594|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1594G>T|||||1594|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*321G>T|||||321|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*321G>T|||||321|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:64,1:64:2381:1:11:0,-18.467,-213.416

+NC_045512.2	1142	.	C	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=141.985;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0865;PAIRED=0;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2404;RO=64;RPL=0;RPP=5.18177;RPPR=3.14602;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.14602;SRR=31;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.877C>G|p.Leu293Val|877/21291|877/21291|293/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.877C>G|p.Leu293Val|877/13218|877/13218|293/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.337C>G|p.Leu113Val|337/1914|337/1914|113/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.337C>G|p.Leu113Val|337/1914|337/1914|113/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1578C>G|||||1578|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1578C>G|||||1578|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*337C>G|||||337|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*337C>G|||||337|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:64,1:64:2404:1:11:0,-18.467,-215.488

+NC_045512.2	1153	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=7.35324;EPPR=139.813;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.2341;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=2338;RO=63;RPL=1;RPP=3.0103;RPPR=3.04477;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=32;SRP=3.04477;SRR=31;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.888T>C|p.Phe296Phe|888/21291|888/21291|296/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.888T>C|p.Phe296Phe|888/13218|888/13218|296/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.348T>C|p.Phe116Phe|348/1914|348/1914|116/637||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.348T>C|p.Phe116Phe|348/1914|348/1914|116/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1567T>C|||||1567|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1567T>C|||||1567|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*348T>C|||||348|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*348T>C|||||348|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:63,2:63:2338:2:76:0,-12.3521,-203.432

+NC_045512.2	1193	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.14602;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.0865;PAIRED=0;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2417;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.14602;SRR=31;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.928A>T|p.Asn310Tyr|928/21291|928/21291|310/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.928A>T|p.Asn310Tyr|928/13218|928/13218|310/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.388A>T|p.Asn130Tyr|388/1914|388/1914|130/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.388A>T|p.Asn130Tyr|388/1914|388/1914|130/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1527A>T|||||1527|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1527A>T|||||1527|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*388A>T|||||388|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*388A>T|||||388|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:64,1:64:2417:1:11:0,-18.467,-216.656

+NC_045512.2	1205	.	C	T	0.0010911	.	AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.289;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=340;QR=2079;RO=56;RPL=9;RPP=22.5536;RPPR=124.613;RPR=0;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.940C>T|p.Gln314*|940/21291|940/21291|314/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.940C>T|p.Gln314*|940/13218|940/13218|314/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.400C>T|p.Gln134*|400/1914|400/1914|134/637||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.400C>T|p.Gln134*|400/1914|400/1914|134/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1515C>T|||||1515|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1515C>T|||||1515|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*400C>T|||||400|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*400C>T|||||400|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:65:56,9:56:2079:9:340:-11.3895,0,-167.79

+NC_045512.2	1213	.	C	T	3.11242E-4	.	AB=0.138462;ABP=76.807;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=3.25157;EPPR=3.16541;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.54346;PAIRED=0.888889;PAIREDR=0.892857;PAO=0;PQA=0;PQR=0;PRO=0;QA=334;QR=2086;RO=56;RPL=9;RPP=22.5536;RPPR=124.613;RPR=0;RUN=1;SAF=4;SAP=3.25157;SAR=5;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.948C>T|p.Cys316Cys|948/21291|948/21291|316/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.948C>T|p.Cys316Cys|948/13218|948/13218|316/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.408C>T|p.Cys136Cys|408/1914|408/1914|136/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.408C>T|p.Cys136Cys|408/1914|408/1914|136/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1507C>T|||||1507|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1507C>T|||||1507|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*408C>T|||||408|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*408C>T|||||408|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:65:56,9:56:2086:9:334:-10.8446,0,-168.42

+NC_045512.2	1222	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.7773;PAIRED=0;PAIREDR=0.90625;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2374;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.957T>C|p.Thr319Thr|957/21291|957/21291|319/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.957T>C|p.Thr319Thr|957/13218|957/13218|319/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.417T>C|p.Thr139Thr|417/1914|417/1914|139/637||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.417T>C|p.Thr139Thr|417/1914|417/1914|139/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1498T>C|||||1498|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1498T>C|||||1498|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*417T>C|||||417|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*417T>C|||||417|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:64,1:64:2374:1:8:0,-18.767,-213.093

+NC_045512.2	1224	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=90.7773;PAIRED=1;PAIREDR=0.890625;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=2363;RO=64;RPL=1;RPP=5.18177;RPPR=141.985;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.0103;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.959T>C|p.Leu320Pro|959/21291|959/21291|320/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.959T>C|p.Leu320Pro|959/13218|959/13218|320/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.419T>C|p.Leu140Pro|419/1914|419/1914|140/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.419T>C|p.Leu140Pro|419/1914|419/1914|140/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1496T>C|||||1496|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1496T>C|||||1496|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*419T>C|||||419|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*419T>C|||||419|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:64,1:64:2363:1:8:0,-18.767,-212.104

+NC_045512.2	1254	.	C	T	4.88136E-8	.	AB=0.121951;ABP=53.9075;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=13.8677;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.3038;PAIRED=0.8;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=189;QR=1353;RO=36;RPL=5;RPP=13.8677;RPPR=22.5536;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=22.5536;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.989C>T|p.Ser330Leu|989/21291|989/21291|330/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.989C>T|p.Ser330Leu|989/13218|989/13218|330/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.449C>T|p.Ser150Leu|449/1914|449/1914|150/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.449C>T|p.Ser150Leu|449/1914|449/1914|150/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1466C>T|||||1466|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1466C>T|||||1466|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*449C>T|||||449|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*449C>T|||||449|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:36,5:36:1353:5:189:-5.03372,0,-109.719

+NC_045512.2	1288	.	C	T	4.88136E-8	.	AB=0.121951;ABP=53.9075;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=13.8677;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.3038;PAIRED=0.8;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=189;QR=1362;RO=36;RPL=5;RPP=13.8677;RPPR=22.5536;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=22.5536;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1023C>T|p.Cys341Cys|1023/21291|1023/21291|341/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1023C>T|p.Cys341Cys|1023/13218|1023/13218|341/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.483C>T|p.Cys161Cys|483/1914|483/1914|161/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.483C>T|p.Cys161Cys|483/1914|483/1914|161/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1432C>T|||||1432|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1432C>T|||||1432|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*483C>T|||||483|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*483C>T|||||483|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:36,5:36:1362:5:189:-5.03372,0,-110.53

+NC_045512.2	1292	.	T	C	0.189044	.	AB=0.170732;ABP=41.6201;AC=1;AF=0.5;AN=2;AO=7;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=18.2106;EPPR=76.8404;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=3.11248;PAIRED=1;PAIREDR=0.882353;PAO=0;PQA=0;PQR=0;PRO=0;QA=266;QR=1290;RO=34;RPL=0;RPP=18.2106;RPPR=60.4905;RPR=7;RUN=1;SAF=7;SAP=18.2106;SAR=0;SRF=2;SRP=60.4905;SRR=32;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1027T>C|p.Phe343Leu|1027/21291|1027/21291|343/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1027T>C|p.Phe343Leu|1027/13218|1027/13218|343/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.487T>C|p.Phe163Leu|487/1914|487/1914|163/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.487T>C|p.Phe163Leu|487/1914|487/1914|163/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1428T>C|||||1428|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1428T>C|||||1428|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*487T>C|||||487|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*487T>C|||||487|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:34,7:34:1290:7:266:-11.9603,0,-104.054

+NC_045512.2	1314	.	C	T	1.71007E-8	.	AB=0.119048;ABP=55.9529;AC=1;AF=0.5;AN=2;AO=5;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=13.8677;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=59.0541;NS=1;NUMALT=1;ODDS=19.3527;PAIRED=0.8;PAIREDR=0.891892;PAO=0;PQA=0;PQR=0;PRO=0;QA=190;QR=1385;RO=37;RPL=5;RPP=13.8677;RPPR=19.9713;RPR=0;RUN=1;SAF=0;SAP=13.8677;SAR=5;SRF=9;SRP=24.1968;SRR=28;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1049C>T|p.Thr350Ile|1049/21291|1049/21291|350/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1049C>T|p.Thr350Ile|1049/13218|1049/13218|350/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.509C>T|p.Thr170Ile|509/1914|509/1914|170/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.509C>T|p.Thr170Ile|509/1914|509/1914|170/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1406C>T|||||1406|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1406C>T|||||1406|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*509C>T|||||509|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*509C>T|||||509|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:42:37,5:37:1385:5:190:-4.82418,0,-111.803

+NC_045512.2	1336	.	T	G	3.36083E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=58.6538;NS=1;NUMALT=1;ODDS=32.9924;PAIRED=1;PAIREDR=0.807692;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=908;RO=26;RPL=1;RPP=5.18177;RPPR=8.35546;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=8.35546;SRR=17;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1071T>G|p.Cys357Trp|1071/21291|1071/21291|357/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1071T>G|p.Cys357Trp|1071/13218|1071/13218|357/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.531T>G|p.Cys177Trp|531/1914|531/1914|177/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.531T>G|p.Cys177Trp|531/1914|531/1914|177/637||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1384T>G|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1384T>G|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*531T>G|||||531|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*531T>G|||||531|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:908:1:34:0,-4.7289,-77.5254

+NC_045512.2	1406	.	G	T	7.97288E-5	.	AB=0.111111;ABP=26.6552;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=7.35324;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.9054;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=581;RO=16;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=3.0103;SRR=8;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1141G>T|p.Glu381*|1141/21291|1141/21291|381/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1141G>T|p.Glu381*|1141/13218|1141/13218|381/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.601G>T|p.Glu201*|601/1914|601/1914|201/637||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.601G>T|p.Glu201*|601/1914|601/1914|201/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1314G>T|||||1314|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1314G>T|||||1314|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*601G>T|||||601|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*601G>T|||||601|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:18:16,2:16:581:2:75:-1.7018,0,-47.2006

+NC_045512.2	1441	.	C	T	366.029	.	AB=0.833333;ABP=20.3821;AC=1;AF=0.5;AN=2;AO=15;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=35.5824;EPPR=9.52472;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.41326;PAIRED=1;PAIREDR=0.666667;PAO=0;PQA=0;PQR=0;PRO=0;QA=567;QR=114;RO=3;RPL=7;RPP=3.15506;RPPR=3.73412;RPR=8;RUN=1;SAF=7;SAP=3.15506;SAR=8;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1176C>T|p.Gly392Gly|1176/21291|1176/21291|392/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1176C>T|p.Gly392Gly|1176/13218|1176/13218|392/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.636C>T|p.Gly212Gly|636/1914|636/1914|212/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.636C>T|p.Gly212Gly|636/1914|636/1914|212/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1279C>T|||||1279|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1279C>T|||||1279|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*636C>T|||||636|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*636C>T|||||636|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:18:3,15:3:114:15:567:-45.9537,0,-5.21381

+NC_045512.2	1456	.	T	C	8.91572E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=645;RO=17;RPL=1;RPP=5.18177;RPPR=3.13803;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=8;SRP=3.13803;SRR=9;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1191T>C|p.Leu397Leu|1191/21291|1191/21291|397/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1191T>C|p.Leu397Leu|1191/13218|1191/13218|397/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.651T>C|p.Leu217Leu|651/1914|651/1914|217/637||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.651T>C|p.Leu217Leu|651/1914|651/1914|217/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1264T>C|||||1264|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1264T>C|||||1264|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*651T>C|||||651|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*651T>C|||||651|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:645:1:38:0,-1.62127,-54.5906

+NC_045512.2	1534	.	G	T	3.33317E-5	.	AB=0.111111;ABP=26.6552;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.7775;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=556;RO=16;RPL=2;RPP=7.35324;RPPR=37.7539;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=3.0103;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1269G>T|p.Trp423Cys|1269/21291|1269/21291|423/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1269G>T|p.Trp423Cys|1269/13218|1269/13218|423/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.729G>T|p.Trp243Cys|729/1914|729/1914|243/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.729G>T|p.Trp243Cys|729/1914|729/1914|243/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1186G>T|||||1186|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1186G>T|||||1186|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*729G>T|||||729|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*729G>T|||||729|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:18:16,2:16:556:2:71:-1.32304,0,-44.9385

+NC_045512.2	1580	.	GTTGG	GTTTGG	1.41193E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=14;DPB=14.2;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.9391;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=488;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=7.18621;SRR=9;TYPE=ins;ANN=GTTTGG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1317dupT|p.Gly440fs|1318/21291|1318/21291|440/7096||,GTTTGG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1317dupT|p.Gly440fs|1318/13218|1318/13218|440/4405||,GTTTGG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.777dupT|p.Gly260fs|778/1914|778/1914|260/637||WARNING_TRANSCRIPT_NO_START_CODON,GTTTGG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.777dupT|p.Gly260fs|778/1914|778/1914|260/637||WARNING_TRANSCRIPT_NO_START_CODON,GTTTGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1138dupT|||||1137|WARNING_TRANSCRIPT_NO_START_CODON,GTTTGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1138dupT|||||1137|WARNING_TRANSCRIPT_NO_START_CODON,GTTTGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*777dupT|||||778|WARNING_TRANSCRIPT_NO_STOP_CODON,GTTTGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*777dupT|||||778|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:488:1:37:0,-0.516591,-40.5677

+NC_045512.2	1601	.	C	T	1.77522E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=494;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=7.18621;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1336C>T|p.Leu446Phe|1336/21291|1336/21291|446/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1336C>T|p.Leu446Phe|1336/13218|1336/13218|446/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.796C>T|p.Leu266Phe|796/1914|796/1914|266/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.796C>T|p.Leu266Phe|796/1914|796/1914|266/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1119C>T|||||1119|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1119C>T|||||1119|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*796C>T|||||796|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*796C>T|||||796|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:494:1:38:0,-0.417151,-41.0105

+NC_045512.2	1609	.	C	T	1.77522E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=494;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=7.18621;SRR=9;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1344C>T|p.Asp448Asp|1344/21291|1344/21291|448/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1344C>T|p.Asp448Asp|1344/13218|1344/13218|448/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.804C>T|p.Asp268Asp|804/1914|804/1914|268/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.804C>T|p.Asp268Asp|804/1914|804/1914|268/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1111C>T|||||1111|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1111C>T|||||1111|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*804C>T|||||804|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*804C>T|||||804|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:494:1:38:0,-0.417151,-41.0105

+NC_045512.2	1684	.	C	T	0.895072	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1.47459;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=269;RO=8;RPL=0;RPP=7.35324;RPPR=20.3821;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1419C>T|p.Ile473Ile|1419/21291|1419/21291|473/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1419C>T|p.Ile473Ile|1419/13218|1419/13218|473/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.879C>T|p.Ile293Ile|879/1914|879/1914|293/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.879C>T|p.Ile293Ile|879/1914|879/1914|293/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1036C>T|||||1036|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1036C>T|||||1036|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*879C>T|||||879|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*879C>T|||||879|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:269:2:73:-3.9208,0,-21.5227

+NC_045512.2	1759	.	A	T	1.58317	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=20.3821;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.821324;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=304;RO=8;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1494A>T|p.Ala498Ala|1494/21291|1494/21291|498/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1494A>T|p.Ala498Ala|1494/13218|1494/13218|498/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.954A>T|p.Ala318Ala|954/1914|954/1914|318/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.954A>T|p.Ala318Ala|954/1914|954/1914|318/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-961A>T|||||961|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-961A>T|||||961|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*954A>T|||||954|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*954A>T|||||954|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:304:2:76:-4.20451,0,-24.7098

+NC_045512.2	1841	.	C	T	1.58317	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=0.821324;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=301;RO=8;RPL=2;RPP=7.35324;RPPR=20.3821;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.0103;SRR=4;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1576C>T|p.Gln526*|1576/21291|1576/21291|526/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1576C>T|p.Gln526*|1576/13218|1576/13218|526/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1036C>T|p.Gln346*|1036/1914|1036/1914|346/637||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1036C>T|p.Gln346*|1036/1914|1036/1914|346/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-879C>T|||||879|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-879C>T|||||879|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1036C>T|||||1036|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1036C>T|||||1036|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:10:8,2:8:301:2:76:-4.20451,0,-24.4375

+NC_045512.2	1883	.	G	A	1.32389E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.6087;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=444;RO=12;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.73412;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1618G>A|p.Ala540Thr|1618/21291|1618/21291|540/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1618G>A|p.Ala540Thr|1618/13218|1618/13218|540/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1078G>A|p.Ala360Thr|1078/1914|1078/1914|360/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1078G>A|p.Ala360Thr|1078/1914|1078/1914|360/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-837G>A|||||837|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-837G>A|||||837|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1078G>A|||||1078|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1078G>A|||||1078|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:444:1:11:0,-2.81339,-39.2047

+NC_045512.2	1902	.	C	T	6.59366E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.398;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=456;RO=12;RPL=1;RPP=5.18177;RPPR=5.9056;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=8;SRP=5.9056;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1637C>T|p.Ser546Leu|1637/21291|1637/21291|546/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1637C>T|p.Ser546Leu|1637/13218|1637/13218|546/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1097C>T|p.Ser366Leu|1097/1914|1097/1914|366/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1097C>T|p.Ser366Leu|1097/1914|1097/1914|366/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-818C>T|||||818|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-818C>T|||||818|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1097C>T|||||1097|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1097C>T|||||1097|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:456:1:38:0,-0.116121,-37.593

+NC_045512.2	1943	.	C	T	6.59366E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.398;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=456;RO=12;RPL=0;RPP=5.18177;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.73412;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1678C>T|p.Arg560Cys|1678/21291|1678/21291|560/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1678C>T|p.Arg560Cys|1678/13218|1678/13218|560/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1138C>T|p.Arg380Cys|1138/1914|1138/1914|380/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1138C>T|p.Arg380Cys|1138/1914|1138/1914|380/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-777C>T|||||777|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-777C>T|||||777|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1138C>T|||||1138|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1138C>T|||||1138|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:456:1:38:0,-0.116121,-37.593

+NC_045512.2	2134	.	A	C	3.80095E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.1592;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=509;RO=14;RPL=1;RPP=5.18177;RPPR=33.4109;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1869A>C|p.Lys623Asn|1869/21291|1869/21291|623/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1869A>C|p.Lys623Asn|1869/13218|1869/13218|623/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1329A>C|p.Lys443Asn|1329/1914|1329/1914|443/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1329A>C|p.Lys443Asn|1329/1914|1329/1914|443/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-586A>C|||||586|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-586A>C|||||586|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1329A>C|||||1329|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1329A>C|||||1329|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:509:1:7:0,-3.81545,-45.4449

+NC_045512.2	2166	.	A	C	3.80095E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.1592;PAIRED=1;PAIREDR=0.928571;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=482;RO=14;RPL=1;RPP=5.18177;RPPR=33.4109;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1901A>C|p.Lys634Thr|1901/21291|1901/21291|634/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1901A>C|p.Lys634Thr|1901/13218|1901/13218|634/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1361A>C|p.Lys454Thr|1361/1914|1361/1914|454/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1361A>C|p.Lys454Thr|1361/1914|1361/1914|454/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-554A>C|||||554|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-554A>C|||||554|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1361A>C|||||1361|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1361A>C|||||1361|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:482:1:7:0,-3.81545,-42.9993

+NC_045512.2	2659	.	G	T	103.718	.	AB=0.4;ABP=4.31318;AC=1;AF=0.5;AN=2;AO=6;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=16.0391;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.882;PAIRED=1;PAIREDR=0.888889;PAO=0;PQA=0;PQR=0;PRO=0;QA=224;QR=342;RO=9;RPL=3;RPP=3.0103;RPPR=3.25157;RPR=3;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=5;SRP=3.25157;SRR=4;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2394G>T|p.Lys798Asn|2394/21291|2394/21291|798/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2394G>T|p.Lys798Asn|2394/13218|2394/13218|798/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1854G>T|p.Lys618Asn|1854/1914|1854/1914|618/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1854G>T|p.Lys618Asn|1854/1914|1854/1914|618/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-61G>T|||||61|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-61G>T|||||61|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1854G>T|||||1854|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1854G>T|||||1854|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:15:9,6:9:342:6:224:-16.0044,0,-26.6222

+NC_045512.2	2714	.	G	C	0.00435058	.	AB=0.133333;ABP=20.5268;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=7.35324;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=6.9055;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=494;RO=13;RPL=1;RPP=3.0103;RPPR=3.17734;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2449G>C|p.Gly817Arg|2449/21291|2449/21291|817/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2449G>C|p.Gly817Arg|2449/13218|2449/13218|817/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1909G>C|p.Gly637Arg|1909/1914|1909/1914|637/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1909G>C|p.Gly637Arg|1909/1914|1909/1914|637/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-6G>C|||||6|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-6G>C|||||6|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1909G>C|||||1909|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1909G>C|||||1909|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:15:13,2:13:494:2:76:-2.69936,0,-40.2923

+NC_045512.2	2719	.	TGC	TC	198.79	.	AB=0.6;ABP=4.31318;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1M1D1M;DP=15;DPB=12;DPRA=0;EPP=22.5536;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.3031;PAIRED=0.888889;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=226;RO=6;RPL=5;RPP=3.25157;RPPR=3.0103;RPR=4;RUN=1;SAF=5;SAP=3.25157;SAR=4;SRF=3;SRP=3.0103;SRR=3;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2455delG|p.Ala819fs|2455/21291|2455/21291|819/7096||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2455delG|p.Ala819fs|2455/13218|2455/13218|819/4405||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1delG|p.Ala1fs|1/5835|1/5835|1/1944||WARNING_TRANSCRIPT_NO_START_CODON,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1delG|p.Ala1fs|1/5835|1/5835|1/1944||WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1915delG|||||1915|WARNING_TRANSCRIPT_NO_STOP_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1915delG|||||1915|WARNING_TRANSCRIPT_NO_STOP_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1delG|||||1|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1delG|||||1|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:15:6,9:6:226:9:342:-26.6222,0,-16.1872

+NC_045512.2	2811	.	T	C	5.82418E-4	.	AB=0.142857;ABP=10.7656;AC=1;AF=0.5;AN=2;AO=1;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.18177;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.91681;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=228;RO=6;RPL=1;RPP=5.18177;RPPR=16.0391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=16.0391;SRR=6;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2546T>C|p.Ile849Thr|2546/21291|2546/21291|849/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2546T>C|p.Ile849Thr|2546/13218|2546/13218|849/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.92T>C|p.Ile31Thr|92/5835|92/5835|31/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.92T>C|p.Ile31Thr|92/5835|92/5835|31/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2006T>C|||||2006|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2006T>C|||||2006|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*92T>C|||||92|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*92T>C|||||92|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7:6,1:6:228:1:24:-0.292681,0,-18.7778

+NC_045512.2	2828	.	G	T	1.90019E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=33.4109;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.9447;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=504;RO=14;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=3.0103;SRR=7;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2563G>T|p.Glu855*|2563/21291|2563/21291|855/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2563G>T|p.Glu855*|2563/13218|2563/13218|855/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.109G>T|p.Glu37*|109/5835|109/5835|37/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.109G>T|p.Glu37*|109/5835|109/5835|37/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2023G>T|||||2023|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2023G>T|||||2023|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*109G>T|||||109|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*109G>T|||||109|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:15:14,1:14:504:1:34:0,-1.11654,-42.2968

+NC_045512.2	2873	.	G	T	2.35276E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3362;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=682;RO=18;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=4.9405;SRR=7;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2608G>T|p.Glu870*|2608/21291|2608/21291|870/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2608G>T|p.Glu870*|2608/13218|2608/13218|870/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.154G>T|p.Glu52*|154/5835|154/5835|52/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.154G>T|p.Glu52*|154/5835|154/5835|52/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2068G>T|||||2068|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2068G>T|||||2068|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*154G>T|||||154|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*154G>T|||||154|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:682:1:38:0,-1.9223,-57.9181

+NC_045512.2	2891	.	GCA	GCCA	2.35276E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I2M;DP=19;DPB=19.3333;DPRA=0;EPP=5.18177;EPPR=33.8935;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.3362;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=677;RO=18;RPL=1;RPP=5.18177;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=4.9405;SRR=7;TYPE=ins;ANN=GCCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2627dupC|p.Asp877fs|2628/21291|2628/21291|876/7096||,GCCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2627dupC|p.Asp877fs|2628/13218|2628/13218|876/4405||,GCCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.173dupC|p.Asp59fs|174/5835|174/5835|58/1944||WARNING_TRANSCRIPT_NO_START_CODON,GCCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.173dupC|p.Asp59fs|174/5835|174/5835|58/1944||WARNING_TRANSCRIPT_NO_START_CODON,GCCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2087dupC|||||2088|WARNING_TRANSCRIPT_NO_STOP_CODON,GCCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2087dupC|||||2088|WARNING_TRANSCRIPT_NO_STOP_CODON,GCCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*173dupC|||||174|WARNING_TRANSCRIPT_NO_START_CODON,GCCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*173dupC|||||174|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:677:1:38:0,-1.9223,-57.4672

+NC_045512.2	2942	.	C	T	8.20418E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.7846;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=735;RO=20;RPL=0;RPP=7.35324;RPPR=46.4397;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2677C>T|p.Leu893Leu|2677/21291|2677/21291|893/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2677C>T|p.Leu893Leu|2677/13218|2677/13218|893/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.223C>T|p.Leu75Leu|223/5835|223/5835|75/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.223C>T|p.Leu75Leu|223/5835|223/5835|75/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2137C>T|||||2137|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2137C>T|||||2137|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*223C>T|||||223|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*223C>T|||||223|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:20,2:20:735:2:67:0,-0.260581,-60.1116

+NC_045512.2	3037	.	C	T	682.489	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=42.4916;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=35.1036;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=831;QR=0;RO=0;RPL=12;RPP=3.40511;RPPR=0;RPR=10;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2772C>T|p.Phe924Phe|2772/13218|2772/13218|924/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.318C>T|p.Phe106Phe|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.318C>T|p.Phe106Phe|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2232C>T|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2232C>T|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*318C>T|||||318|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*318C>T|||||318|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:22:0,22:0:0:22:831:-75.1154,-6.62266,0

+NC_045512.2	3061	.	A	G	1.70196E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=5.59539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2658;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=760;RO=21;RPL=1;RPP=5.18177;RPPR=32.8939;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=11;SRP=3.1137;SRR=10;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2796A>G|p.Glu932Glu|2796/21291|2796/21291|932/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2796A>G|p.Glu932Glu|2796/13218|2796/13218|932/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.342A>G|p.Glu114Glu|342/5835|342/5835|114/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.342A>G|p.Glu114Glu|342/5835|342/5835|114/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2256A>G|||||2256|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2256A>G|||||2256|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*342A>G|||||342|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*342A>G|||||342|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:760:1:34:0,-3.22375,-65.3167

+NC_045512.2	3073	.	TGAAGAAGAAGAGT	TGAAGAAGAGT	5.84477E-7	.	AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1M3D10M;DP=22;DPB=21.5714;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=3;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.8211;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=725;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=del;ANN=TGAAGAAGAGT|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2817_2819delAGA|p.Glu940del|2817/21291|2817/21291|939/7096||,TGAAGAAGAGT|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2817_2819delAGA|p.Glu940del|2817/13218|2817/13218|939/4405||,TGAAGAAGAGT|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.363_365delAGA|p.Glu122del|363/5835|363/5835|121/1944||WARNING_TRANSCRIPT_NO_START_CODON,TGAAGAAGAGT|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.363_365delAGA|p.Glu122del|363/5835|363/5835|121/1944||WARNING_TRANSCRIPT_NO_START_CODON,TGAAGAAGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2277_*2279delAGA|||||2277|WARNING_TRANSCRIPT_NO_STOP_CODON,TGAAGAAGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2277_*2279delAGA|||||2277|WARNING_TRANSCRIPT_NO_STOP_CODON,TGAAGAAGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*363_*365delAGA|||||363|WARNING_TRANSCRIPT_NO_START_CODON,TGAAGAAGAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*363_*365delAGA|||||363|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:22:20,2:20:725:2:76:-0.592151,0,-58.9509

+NC_045512.2	3105	.	A	G	4.70219E-7	.	AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.0386;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=700;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2840A>G|p.Tyr947Cys|2840/21291|2840/21291|947/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2840A>G|p.Tyr947Cys|2840/13218|2840/13218|947/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.386A>G|p.Tyr129Cys|386/5835|386/5835|129/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.386A>G|p.Tyr129Cys|386/5835|386/5835|129/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2300A>G|||||2300|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2300A>G|||||2300|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*386A>G|||||386|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*386A>G|||||386|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:22:20,2:20:700:2:75:-0.497684,0,-56.6876

+NC_045512.2	3110	.	T	C	5.9668E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=3.1137;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.0197;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=788;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=10;SRP=3.1137;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2845T>C|p.Tyr949His|2845/21291|2845/21291|949/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2845T>C|p.Tyr949His|2845/13218|2845/13218|949/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.391T>C|p.Tyr131His|391/5835|391/5835|131/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.391T>C|p.Tyr131His|391/5835|391/5835|131/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2305T>C|||||2305|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2305T>C|||||2305|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*391T>C|||||391|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*391T>C|||||391|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:788:1:9:0,-5.72266,-70.3482

+NC_045512.2	3113	.	G	T	5.84477E-7	.	AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.8211;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=713;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2848G>T|p.Gly950Cys|2848/21291|2848/21291|950/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2848G>T|p.Gly950Cys|2848/13218|2848/13218|950/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.394G>T|p.Gly132Cys|394/5835|394/5835|132/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.394G>T|p.Gly132Cys|394/5835|394/5835|132/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2308G>T|||||2308|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2308G>T|||||2308|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*394G>T|||||394|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*394G>T|||||394|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:22:20,2:20:713:2:76:-0.592151,0,-57.8648

+NC_045512.2	3118	.	T	A	2.44527E-7	.	AB=0.0909091;ABP=34.9902;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.6925;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=668;RO=20;RPL=2;RPP=7.35324;RPPR=46.4397;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2853T>A|p.Thr951Thr|2853/21291|2853/21291|951/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2853T>A|p.Thr951Thr|2853/13218|2853/13218|951/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.399T>A|p.Thr133Thr|399/5835|399/5835|133/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.399T>A|p.Thr133Thr|399/5835|399/5835|133/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2313T>A|||||2313|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2313T>A|||||2313|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*399T>A|||||399|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*399T>A|||||399|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:22:20,2:20:668:2:72:-0.213711,0,-53.7961

+NC_045512.2	3244	.	C	A	4.31238E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.0103;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1143;PAIRED=1;PAIREDR=0.969697;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1214;RO=33;RPL=0;RPP=7.35324;RPPR=74.6689;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2979C>A|p.Gly993Gly|2979/21291|2979/21291|993/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2979C>A|p.Gly993Gly|2979/13218|2979/13218|993/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.525C>A|p.Gly175Gly|525/5835|525/5835|175/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.525C>A|p.Gly175Gly|525/5835|525/5835|175/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2439C>A|||||2439|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2439C>A|||||2439|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*525C>A|||||525|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*525C>A|||||525|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:35:33,2:33:1214:2:75:0,-3.41571,-102.438

+NC_045512.2	3267	.	C	T	1053.59	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=35;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=3.07234;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=53.1255;PAIRED=0.971429;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1304;QR=0;RO=0;RPL=0;RPP=79.0118;RPPR=0;RPR=35;RUN=1;SAF=17;SAP=3.07234;SAR=18;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3002C>T|p.Thr1001Ile|3002/21291|3002/21291|1001/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3002C>T|p.Thr1001Ile|3002/13218|3002/13218|1001/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.548C>T|p.Thr183Ile|548/5835|548/5835|183/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.548C>T|p.Thr183Ile|548/5835|548/5835|183/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2462C>T|||||2462|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2462C>T|||||2462|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*548C>T|||||548|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*548C>T|||||548|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:35:0,35:0:0:35:1304:-117.653,-10.5361,0

+NC_045512.2	3462	.	A	C	1.99799E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=5.18177;EPPR=48.9587;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.1744;PAIRED=1;PAIREDR=0.96;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=925;RO=25;RPL=0;RPP=5.18177;RPPR=17.6895;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=7;SRP=13.5202;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3197A>C|p.Lys1066Thr|3197/21291|3197/21291|1066/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3197A>C|p.Lys1066Thr|3197/13218|3197/13218|1066/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.743A>C|p.Lys248Thr|743/5835|743/5835|248/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.743A>C|p.Lys248Thr|743/5835|743/5835|248/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2657A>C|||||2657|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2657A>C|||||2657|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*743A>C|||||743|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*743A>C|||||743|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:25,1:25:925:1:23:0,-5.52687,-81.2678

+NC_045512.2	3464	.	C	A	2.15924E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=53.2759;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=982;RO=27;RPL=0;RPP=5.18177;RPPR=12.7417;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=9.52472;SRR=18;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3199C>A|p.His1067Asn|3199/21291|3199/21291|1067/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3199C>A|p.His1067Asn|3199/13218|3199/13218|1067/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.745C>A|p.His249Asn|745/5835|745/5835|249/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.745C>A|p.His249Asn|745/5835|745/5835|249/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2659C>A|||||2659|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2659C>A|||||2659|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*745C>A|||||745|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*745C>A|||||745|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:982:1:34:0,-5.02993,-85.2914

+NC_045512.2	3465	.	A	C	8.04008E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=7.35324;EPPR=59.4686;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5855;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=46;QR=954;RO=26;RPL=0;RPP=7.35324;RPPR=11.3621;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=8;SRP=11.3621;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3200A>C|p.His1067Pro|3200/21291|3200/21291|1067/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3200A>C|p.His1067Pro|3200/13218|3200/13218|1067/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.746A>C|p.His249Pro|746/5835|746/5835|249/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.746A>C|p.His249Pro|746/5835|746/5835|249/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2660A>C|||||2660|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2660A>C|||||2660|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*746A>C|||||746|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*746A>C|||||746|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:26,2:26:954:2:46:0,-4.05988,-81.806

+NC_045512.2	3528	.	A	T	3.52281E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=70.3259;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.754;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1113;RO=31;RPL=1;RPP=5.18177;RPPR=3.08035;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3263A>T|p.Asp1088Val|3263/21291|3263/21291|1088/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3263A>T|p.Asp1088Val|3263/13218|3263/13218|1088/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.809A>T|p.Asp270Val|809/5835|809/5835|270/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.809A>T|p.Asp270Val|809/5835|809/5835|270/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2723A>T|||||2723|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2723A>T|||||2723|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*809A>T|||||809|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*809A>T|||||809|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1113:1:34:0,-6.23405,-97.0776

+NC_045512.2	3529	.	T	G	2.61878E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=7.35324;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.0666;PAIRED=0.5;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=39;QR=1050;RO=29;RPL=2;RPP=7.35324;RPPR=3.68421;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=16;SRP=3.68421;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3264T>G|p.Asp1088Glu|3264/21291|3264/21291|1088/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3264T>G|p.Asp1088Glu|3264/13218|3264/13218|1088/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.810T>G|p.Asp270Glu|810/5835|810/5835|270/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.810T>G|p.Asp270Glu|810/5835|810/5835|270/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2724T>G|||||2724|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2724T>G|||||2724|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*810T>G|||||810|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*810T>G|||||810|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:29,2:29:1050:2:39:0,-5.62714,-91.105

+NC_045512.2	3562	.	G	T	9.89491E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.1374;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1042;RO=30;RPL=0;RPP=7.35324;RPPR=68.1545;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3297G>T|p.Val1099Val|3297/21291|3297/21291|1099/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3297G>T|p.Val1099Val|3297/13218|3297/13218|1099/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.843G>T|p.Val281Val|843/5835|843/5835|281/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.843G>T|p.Val281Val|843/5835|843/5835|281/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4993G>T|||||4993|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4993G>T|||||4993|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2757G>T|||||2757|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2757G>T|||||2757|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*843G>T|||||843|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*843G>T|||||843|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:30,2:30:1042:2:75:0,-2.51262,-86.9511

+NC_045512.2	3647	.	ATTCA	ATCA	1.19167E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D3M;DP=32;DPB=31.6;DPRA=0;EPP=7.35324;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=28.9199;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1121;RO=30;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.0103;SRR=15;TYPE=del;ANN=ATCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3384delT|p.Gln1129fs|3384/21291|3384/21291|1128/7096||,ATCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3384delT|p.Gln1129fs|3384/13218|3384/13218|1128/4405||,ATCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.930delT|p.Gln311fs|930/5835|930/5835|310/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATCA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.930delT|p.Gln311fs|930/5835|930/5835|310/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4906delT|||||4906|WARNING_TRANSCRIPT_NO_START_CODON,ATCA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4906delT|||||4906|WARNING_TRANSCRIPT_NO_START_CODON,ATCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2844delT|||||2844|WARNING_TRANSCRIPT_NO_STOP_CODON,ATCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2844delT|||||2844|WARNING_TRANSCRIPT_NO_STOP_CODON,ATCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*930delT|||||930|WARNING_TRANSCRIPT_NO_START_CODON,ATCA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*930delT|||||930|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:30,2:30:1121:2:76:0,-2.41815,-93.9829

+NC_045512.2	3728	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.7382;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1142;RO=31;RPL=1;RPP=5.18177;RPPR=70.3259;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=15;SRP=3.08035;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3463G>T|p.Gly1155Cys|3463/21291|3463/21291|1155/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3463G>T|p.Gly1155Cys|3463/13218|3463/13218|1155/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1009G>T|p.Gly337Cys|1009/5835|1009/5835|337/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1009G>T|p.Gly337Cys|1009/5835|1009/5835|337/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4827G>T|||||4827|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4827G>T|||||4827|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2923G>T|||||2923|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2923G>T|||||2923|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1009G>T|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1009G>T|||||1009|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1142:1:8:0,-8.83296,-102.283

+NC_045512.2	4060	.	A	C	2.8418E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=42.621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.046;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1077;RO=29;RPL=0;RPP=5.18177;RPPR=24.6501;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=26;SRP=42.621;SRR=3;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3795A>C|p.Pro1265Pro|3795/21291|3795/21291|1265/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3795A>C|p.Pro1265Pro|3795/13218|3795/13218|1265/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1341A>C|p.Pro447Pro|1341/5835|1341/5835|447/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1341A>C|p.Pro447Pro|1341/5835|1341/5835|447/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4495A>C|||||4495|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4495A>C|||||4495|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3255A>C|||||3255|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3255A>C|||||3255|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1341A>C|||||1341|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1341A>C|||||1341|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1077:1:34:0,-5.63199,-93.8409

+NC_045512.2	4126	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=3.0103;EPPR=4.03458;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.9256;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1938;RO=53;RPL=0;RPP=7.35324;RPPR=93.5156;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=26;SRP=3.05127;SRR=27;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3861G>T|p.Val1287Val|3861/21291|3861/21291|1287/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3861G>T|p.Val1287Val|3861/13218|3861/13218|1287/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1407G>T|p.Val469Val|1407/5835|1407/5835|469/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1407G>T|p.Val469Val|1407/5835|1407/5835|469/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4429G>T|||||4429|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4429G>T|||||4429|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3321G>T|||||3321|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3321G>T|||||3321|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1407G>T|||||1407|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1407G>T|||||1407|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:53,2:53:1938:2:75:0,-9.43631,-167.557

+NC_045512.2	4142	.	G	A	6.61515E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=3.16006;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.7866;PAIRED=0;PAIREDR=0.982759;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=2071;RO=58;RPL=0;RPP=5.18177;RPPR=104.246;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.60933;SRR=31;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3877G>A|p.Glu1293Lys|3877/21291|3877/21291|1293/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3877G>A|p.Glu1293Lys|3877/13218|3877/13218|1293/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1423G>A|p.Glu475Lys|1423/5835|1423/5835|475/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1423G>A|p.Glu475Lys|1423/5835|1423/5835|475/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4413G>A|||||4413|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4413G>A|||||4413|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3337G>A|||||3337|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3337G>A|||||3337|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1423G>A|||||1423|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1423G>A|||||1423|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:59:58,1:58:2071:1:7:0,-17.0608,-185.929

+NC_045512.2	4163	.	G	T	5.12534E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=58;DPB=58;DPRA=0;EPP=5.18177;EPPR=3.0484;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.203;PAIRED=1;PAIREDR=0.964912;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2120;RO=57;RPL=1;RPP=5.18177;RPPR=118.251;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=27;SRP=3.35316;SRR=30;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3898G>T|p.Val1300Phe|3898/21291|3898/21291|1300/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3898G>T|p.Val1300Phe|3898/13218|3898/13218|1300/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1444G>T|p.Val482Phe|1444/5835|1444/5835|482/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1444G>T|p.Val482Phe|1444/5835|1444/5835|482/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4392G>T|||||4392|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4392G>T|||||4392|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3358G>T|||||3358|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3358G>T|||||3358|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1444G>T|||||1444|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1444G>T|||||1444|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:58:57,1:57:2120:1:34:0,-14.0608,-187.646

+NC_045512.2	4304	.	A	T	7.3231E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=3.93042;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.9416;PAIRED=1;PAIREDR=0.966102;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2177;RO=59;RPL=0;RPP=5.18177;RPPR=106.394;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=30;SRP=3.0471;SRR=29;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4039A>T|p.Lys1347*|4039/21291|4039/21291|1347/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4039A>T|p.Lys1347*|4039/13218|4039/13218|1347/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1585A>T|p.Lys529*|1585/5835|1585/5835|529/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1585A>T|p.Lys529*|1585/5835|1585/5835|529/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4251A>T|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4251A>T|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3499A>T|||||3499|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3499A>T|||||3499|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1585A>T|||||1585|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1585A>T|||||1585|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:60:59,1:59:2177:1:34:0,-14.6629,-192.771

+NC_045512.2	4391	.	C	T	2.89298E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=50.3001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1356;RO=36;RPL=1;RPP=5.18177;RPPR=27.1378;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=50.3001;SRR=32;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4126C>T|p.Arg1376*|4126/21291|4126/21291|1376/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4126C>T|p.Arg1376*|4126/13218|4126/13218|1376/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1672C>T|p.Arg558*|1672/5835|1672/5835|558/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1672C>T|p.Arg558*|1672/5835|1672/5835|558/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4164C>T|||||4164|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4164C>T|||||4164|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3586C>T|||||3586|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3586C>T|||||3586|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1672C>T|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1672C>T|||||1672|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1356:1:38:0,-7.34084,-118.536

+NC_045512.2	4397	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=50.3001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.5403;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1364;RO=36;RPL=1;RPP=5.18177;RPPR=27.1378;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=50.3001;SRR=32;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4132A>G|p.Met1378Val|4132/21291|4132/21291|1378/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4132A>G|p.Met1378Val|4132/13218|4132/13218|1378/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1678A>G|p.Met560Val|1678/5835|1678/5835|560/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1678A>G|p.Met560Val|1678/5835|1678/5835|560/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4158A>G|||||4158|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4158A>G|||||4158|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3592A>G|||||3592|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3592A>G|||||3592|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1678A>G|||||1678|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1678A>G|||||1678|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1364:1:34:0,-7.7392,-119.653

+NC_045512.2	4404	.	C	A	2.89298E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=50.3001;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1342;RO=36;RPL=1;RPP=5.18177;RPPR=27.1378;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=50.3001;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4139C>A|p.Ala1380Glu|4139/21291|4139/21291|1380/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4139C>A|p.Ala1380Glu|4139/13218|4139/13218|1380/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1685C>A|p.Ala562Glu|1685/5835|1685/5835|562/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1685C>A|p.Ala562Glu|1685/5835|1685/5835|562/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4151C>A|||||4151|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4151C>A|||||4151|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3599C>A|||||3599|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3599C>A|||||3599|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1685C>A|||||1685|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1685C>A|||||1685|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1342:1:38:0,-7.34084,-117.273

+NC_045512.2	4751	.	A	C	1.35112E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.496;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1051;RO=28;RPL=0;RPP=7.35324;RPPR=63.8115;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4486A>C|p.Thr1496Pro|4486/21291|4486/21291|1496/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4486A>C|p.Thr1496Pro|4486/13218|4486/13218|1496/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2032A>C|p.Thr678Pro|2032/5835|2032/5835|678/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2032A>C|p.Thr678Pro|2032/5835|2032/5835|678/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3804A>C|||||3804|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3804A>C|||||3804|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3946A>C|||||3946|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3946A>C|||||3946|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2032A>C|||||2032|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2032A>C|||||2032|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:28,2:28:1051:2:75:0,-1.91056,-87.7804

+NC_045512.2	4850	.	A	C	1.68301E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=7.35324;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2785;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1064;RO=28;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4585A>C|p.Lys1529Gln|4585/21291|4585/21291|1529/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4585A>C|p.Lys1529Gln|4585/13218|4585/13218|1529/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2131A>C|p.Lys711Gln|2131/5835|2131/5835|711/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2131A>C|p.Lys711Gln|2131/5835|2131/5835|711/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3705A>C|||||3705|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3705A>C|||||3705|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4045A>C|||||4045|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4045A>C|||||4045|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2131A>C|||||2131|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2131A>C|||||2131|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:28,2:28:1064:2:76:0,-1.81609,-88.8561

+NC_045512.2	4890	.	C	A	1.35112E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.496;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1050;RO=28;RPL=2;RPP=7.35324;RPPR=63.8115;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=14;SRP=3.0103;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4625C>A|p.Thr1542Asn|4625/21291|4625/21291|1542/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4625C>A|p.Thr1542Asn|4625/13218|4625/13218|1542/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2171C>A|p.Thr724Asn|2171/5835|2171/5835|724/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2171C>A|p.Thr724Asn|2171/5835|2171/5835|724/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3665C>A|||||3665|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3665C>A|||||3665|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4085C>A|||||4085|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4085C>A|||||4085|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2171C>A|||||2171|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2171C>A|||||2171|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:28,2:28:1050:2:75:0,-1.91056,-87.6907

+NC_045512.2	5014	.	T	G	9.40218E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=5.18177;EPPR=42.0968;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.2535;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=640;RO=18;RPL=1;RPP=5.18177;RPPR=4.9405;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=4.9405;SRR=11;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4749T>G|p.Val1583Val|4749/21291|4749/21291|1583/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4749T>G|p.Val1583Val|4749/13218|4749/13218|1583/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2295T>G|p.Val765Val|2295/5835|2295/5835|765/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2295T>G|p.Val765Val|2295/5835|2295/5835|765/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3541T>G|||||3541|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3541T>G|||||3541|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4209T>G|||||4209|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4209T>G|||||4209|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2295T>G|||||2295|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2295T>G|||||2295|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:19:18,1:18:640:1:34:0,-2.32066,-54.5285

+NC_045512.2	5016	.	T	G	1.34597E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=29.6108;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5921;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=575;RO=16;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.55317;SRR=9;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4751T>G|p.Val1584Gly|4751/21291|4751/21291|1584/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4751T>G|p.Val1584Gly|4751/13218|4751/13218|1584/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2297T>G|p.Val766Gly|2297/5835|2297/5835|766/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2297T>G|p.Val766Gly|2297/5835|2297/5835|766/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3539T>G|||||3539|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3539T>G|||||3539|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4211T>G|||||4211|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4211T>G|||||4211|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2297T>G|||||2297|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2297T>G|||||2297|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:575:1:34:0,-1.7186,-48.6833

+NC_045512.2	5037	.	G	A	40.1272	.	AB=0.285714;ABP=8.59409;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=9.23953;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=146;QR=353;RO=10;RPL=0;RPP=11.6962;RPPR=24.725;RPR=4;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=5;SRP=3.0103;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4772G>A|p.Gly1591Glu|4772/21291|4772/21291|1591/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4772G>A|p.Gly1591Glu|4772/13218|4772/13218|1591/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2318G>A|p.Gly773Glu|2318/5835|2318/5835|773/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2318G>A|p.Gly773Glu|2318/5835|2318/5835|773/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3518G>A|||||3518|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3518G>A|||||3518|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4232G>A|||||4232|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4232G>A|||||4232|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2318G>A|||||2318|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2318G>A|||||2318|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:14:10,4:10:353:4:146:-9.28272,0,-27.8893

+NC_045512.2	5172	.	A	G	3.56433E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9208;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=494;RO=13;RPL=1;RPP=5.18177;RPPR=31.2394;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=3.17734;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4907A>G|p.His1636Arg|4907/21291|4907/21291|1636/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4907A>G|p.His1636Arg|4907/13218|4907/13218|1636/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2453A>G|p.His818Arg|2453/5835|2453/5835|818/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2453A>G|p.His818Arg|2453/5835|2453/5835|818/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3383A>G|||||3383|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3383A>G|||||3383|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4883A>G|||||4883|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4883A>G|||||4883|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4367A>G|||||4367|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4367A>G|||||4367|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2453A>G|||||2453|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2453A>G|||||2453|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:494:1:11:0,-3.11442,-43.7078

+NC_045512.2	5267	.	A	T	3.19931E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2968;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=892;RO=24;RPL=0;RPP=5.18177;RPPR=12.0581;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=12.0581;SRR=7;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5002A>T|p.Lys1668*|5002/21291|5002/21291|1668/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5002A>T|p.Lys1668*|5002/13218|5002/13218|1668/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2548A>T|p.Lys850*|2548/5835|2548/5835|850/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2548A>T|p.Lys850*|2548/5835|2548/5835|850/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3288A>T|||||3288|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3288A>T|||||3288|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4788A>T|||||4788|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4788A>T|||||4788|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4462A>T|||||4462|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4462A>T|||||4462|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2548A>T|||||2548|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2548A>T|||||2548|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:892:1:34:0,-4.12684,-77.2009

+NC_045512.2	5289	.	A	T	3.73074E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=29;DPB=29;DPRA=0;EPP=5.18177;EPPR=63.8115;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.7763;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1057;RO=28;RPL=0;RPP=5.18177;RPPR=18.2106;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=18.2106;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5024A>T|p.Tyr1675Phe|5024/21291|5024/21291|1675/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5024A>T|p.Tyr1675Phe|5024/13218|5024/13218|1675/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2570A>T|p.Tyr857Phe|2570/5835|2570/5835|857/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2570A>T|p.Tyr857Phe|2570/5835|2570/5835|857/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3266A>T|||||3266|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3266A>T|||||3266|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4766A>T|||||4766|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4766A>T|||||4766|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4484A>T|||||4484|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4484A>T|||||4484|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2570A>T|||||2570|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2570A>T|||||2570|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:29:28,1:28:1057:1:38:0,-4.9326,-91.6435

+NC_045512.2	5360	.	T	C	1.21146E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1273;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1551;RO=42;RPL=0;RPP=7.35324;RPPR=94.2121;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5095T>C|p.Tyr1699His|5095/21291|5095/21291|1699/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5095T>C|p.Tyr1699His|5095/13218|5095/13218|1699/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2641T>C|p.Tyr881His|2641/5835|2641/5835|881/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2641T>C|p.Tyr881His|2641/5835|2641/5835|881/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3195T>C|||||3195|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3195T>C|||||3195|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4695T>C|||||4695|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4695T>C|||||4695|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4555T>C|||||4555|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4555T>C|||||4555|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2641T>C|||||2641|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2641T>C|||||2641|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:42,2:42:1551:2:75:0,-6.12498,-132.75

+NC_045512.2	5367	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.9098;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1513;RO=42;RPL=0;RPP=7.35324;RPPR=94.2121;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5102G>T|p.Arg1701Ile|5102/21291|5102/21291|1701/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5102G>T|p.Arg1701Ile|5102/13218|5102/13218|1701/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2648G>T|p.Arg883Ile|2648/5835|2648/5835|883/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2648G>T|p.Arg883Ile|2648/5835|2648/5835|883/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3188G>T|||||3188|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3188G>T|||||3188|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4688G>T|||||4688|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4688G>T|||||4688|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4562G>T|||||4562|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4562G>T|||||4562|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2648G>T|||||2648|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2648G>T|||||2648|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:42,2:42:1513:2:76:0,-6.03051,-129.224

+NC_045512.2	5368	.	A	G	1.12861E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1573;RO=43;RPL=0;RPP=5.18177;RPPR=96.3836;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=3.0608;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5103A>G|p.Arg1701Arg|5103/21291|5103/21291|1701/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5103A>G|p.Arg1701Arg|5103/13218|5103/13218|1701/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2649A>G|p.Arg883Arg|2649/5835|2649/5835|883/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2649A>G|p.Arg883Arg|2649/5835|2649/5835|883/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3187A>G|||||3187|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3187A>G|||||3187|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4687A>G|||||4687|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4687A>G|||||4687|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4563A>G|||||4563|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4563A>G|||||4563|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2649A>G|||||2649|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2649A>G|||||2649|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1573:1:9:0,-12.3453,-140.947

+NC_045512.2	5376	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.9098;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1536;RO=42;RPL=0;RPP=7.35324;RPPR=94.2121;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5111C>A|p.Ala1704Asp|5111/21291|5111/21291|1704/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5111C>A|p.Ala1704Asp|5111/13218|5111/13218|1704/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2657C>A|p.Ala886Asp|2657/5835|2657/5835|886/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2657C>A|p.Ala886Asp|2657/5835|2657/5835|886/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3179C>A|||||3179|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3179C>A|||||3179|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4679C>A|||||4679|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4679C>A|||||4679|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4571C>A|||||4571|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4571C>A|||||4571|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2657C>A|||||2657|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2657C>A|||||2657|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:42,2:42:1536:2:76:0,-6.03051,-131.304

+NC_045512.2	5388	.	C	A	798.742	.	AB=0.727273;ABP=22.751;AC=1;AF=0.5;AN=2;AO=32;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.6329;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1212;QR=439;RO=12;RPL=0;RPP=72.4974;RPPR=29.068;RPR=32;RUN=1;SAF=16;SAP=3.0103;SAR=16;SRF=6;SRP=3.0103;SRR=6;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5123C>A|p.Ala1708Asp|5123/21291|5123/21291|1708/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5123C>A|p.Ala1708Asp|5123/13218|5123/13218|1708/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2669C>A|p.Ala890Asp|2669/5835|2669/5835|890/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2669C>A|p.Ala890Asp|2669/5835|2669/5835|890/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3167C>A|||||3167|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3167C>A|||||3167|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4667C>A|||||4667|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4667C>A|||||4667|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4583C>A|||||4583|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4583C>A|||||4583|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2669C>A|||||2669|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2669C>A|||||2669|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:44:12,32:12:439:32:1212:-96.1364,0,-26.605

+NC_045512.2	5489	.	G	T	1.21146E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=3.0103;EPPR=85.7331;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1273;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1573;RO=42;RPL=2;RPP=7.35324;RPPR=3.21711;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0103;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5224G>T|p.Asp1742Tyr|5224/21291|5224/21291|1742/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5224G>T|p.Asp1742Tyr|5224/13218|5224/13218|1742/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2770G>T|p.Asp924Tyr|2770/5835|2770/5835|924/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2770G>T|p.Asp924Tyr|2770/5835|2770/5835|924/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3066G>T|||||3066|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3066G>T|||||3066|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4566G>T|||||4566|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4566G>T|||||4566|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4684G>T|||||4684|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4684G>T|||||4684|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2770G>T|||||2770|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2770G>T|||||2770|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:42,2:42:1573:2:75:0,-6.12498,-134.726

+NC_045512.2	5523	.	A	C	8.61891E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.5948;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1575;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5258A>C|p.Lys1753Thr|5258/21291|5258/21291|1753/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5258A>C|p.Lys1753Thr|5258/13218|5258/13218|1753/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2804A>C|p.Lys935Thr|2804/5835|2804/5835|935/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2804A>C|p.Lys935Thr|2804/5835|2804/5835|935/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3032A>C|||||3032|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3032A>C|||||3032|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4532A>C|||||4532|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4532A>C|||||4532|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4718A>C|||||4718|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4718A>C|||||4718|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2804A>C|||||2804|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2804A>C|||||2804|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1575:1:10:0,-12.2453,-141.027

+NC_045512.2	5544	.	C	A	1.12861E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1552;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5279C>A|p.Thr1760Lys|5279/21291|5279/21291|1760/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5279C>A|p.Thr1760Lys|5279/13218|5279/13218|1760/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2825C>A|p.Thr942Lys|2825/5835|2825/5835|942/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2825C>A|p.Thr942Lys|2825/5835|2825/5835|942/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3011C>A|||||3011|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3011C>A|||||3011|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4511C>A|||||4511|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4511C>A|||||4511|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4739C>A|||||4739|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4739C>A|||||4739|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2825C>A|||||2825|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2825C>A|||||2825|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1552:1:9:0,-12.3453,-139.057

+NC_045512.2	5546	.	A	C	1.12861E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=61.8251;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1541;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5281A>C|p.Thr1761Pro|5281/21291|5281/21291|1761/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5281A>C|p.Thr1761Pro|5281/13218|5281/13218|1761/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2827A>C|p.Thr943Pro|2827/5835|2827/5835|943/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2827A>C|p.Thr943Pro|2827/5835|2827/5835|943/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3009A>C|||||3009|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3009A>C|||||3009|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4509A>C|||||4509|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4509A>C|||||4509|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4741A>C|||||4741|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4741A>C|||||4741|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2827A>C|||||2827|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2827A>C|||||2827|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1541:1:9:0,-12.3453,-138.068

+NC_045512.2	5553	.	A	C	8.30273E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.0553;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1557;RO=43;RPL=1;RPP=5.18177;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5288A>C|p.Lys1763Thr|5288/21291|5288/21291|1763/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5288A>C|p.Lys1763Thr|5288/13218|5288/13218|1763/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2834A>C|p.Lys945Thr|2834/5835|2834/5835|945/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2834A>C|p.Lys945Thr|2834/5835|2834/5835|945/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3002A>C|||||3002|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3002A>C|||||3002|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4502A>C|||||4502|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4502A>C|||||4502|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4748A>C|||||4748|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4748A>C|||||4748|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2834A>C|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2834A>C|||||2834|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1557:1:8:0,-12.4453,-139.607

+NC_045512.2	5641	.	A	G	3.1823E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1067;RO=30;RPL=1;RPP=5.18177;RPPR=5.61607;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=12;SRP=5.61607;SRR=18;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5376A>G|p.Gln1792Gln|5376/21291|5376/21291|1792/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5376A>G|p.Gln1792Gln|5376/13218|5376/13218|1792/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2922A>G|p.Gln974Gln|2922/5835|2922/5835|974/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2922A>G|p.Gln974Gln|2922/5835|2922/5835|974/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2914A>G|||||2914|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2914A>G|||||2914|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4414A>G|||||4414|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4414A>G|||||4414|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4836A>G|||||4836|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4836A>G|||||4836|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2922A>G|||||2922|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2922A>G|||||2922|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1067:1:34:0,-5.93302,-92.9399

+NC_045512.2	5824	.	T	G	2.95401E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1313;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=828;RO=22;RPL=1;RPP=5.18177;RPPR=50.7827;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=3.0103;SRR=11;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5559T>G|p.Leu1853Leu|5559/21291|5559/21291|1853/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5559T>G|p.Leu1853Leu|5559/13218|5559/13218|1853/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3105T>G|p.Leu1035Leu|3105/5835|3105/5835|1035/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3105T>G|p.Leu1035Leu|3105/5835|3105/5835|1035/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2731T>G|||||2731|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2731T>G|||||2731|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4231T>G|||||4231|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4231T>G|||||4231|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3105T>G|||||3105|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3105T>G|||||3105|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:828:1:10:0,-5.92369,-73.8461

+NC_045512.2	5852	.	ATTAC	ATAC,ACTAC	3.07172E-7	.	AB=0.0869565,0.0434783;ABP=37.093,44.6459;AC=1,0;AF=0.5,0;AN=2;AO=2,1;CIGAR=1M1D3M,1M1X3M;DP=23;DPB=22.6;DPRA=0,0;EPP=3.0103,5.18177;EPPR=3.0103;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=16.4644;PAIRED=1,0;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=75,9;QR=726;RO=20;RPL=2,1;RPP=7.35324,5.18177;RPPR=46.4397;RPR=0,0;RUN=1,1;SAF=1,1;SAP=3.0103,5.18177;SAR=1,0;SRF=10;SRP=3.0103;SRR=10;TYPE=del,snp;ANN=ATAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5589delT|p.Thr1864fs|5589/21291|5589/21291|1863/7096||,ATAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5589delT|p.Thr1864fs|5589/13218|5589/13218|1863/4405||,ATAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3135delT|p.Thr1046fs|3135/5835|3135/5835|1045/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATAC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3135delT|p.Thr1046fs|3135/5835|3135/5835|1045/1944||WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5588T>C|p.Ile1863Thr|5588/21291|5588/21291|1863/7096||,ACTAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5588T>C|p.Ile1863Thr|5588/13218|5588/13218|1863/4405||,ACTAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3134T>C|p.Ile1045Thr|3134/5835|3134/5835|1045/1944||WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3134T>C|p.Ile1045Thr|3134/5835|3134/5835|1045/1944||WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2702T>C|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,ATAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2701delT|||||2701|WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2702T>C|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,ATAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2701delT|||||2701|WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4202T>C|||||4202|WARNING_TRANSCRIPT_NO_START_CODON,ATAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4201delT|||||4201|WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4202T>C|||||4202|WARNING_TRANSCRIPT_NO_START_CODON,ATAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4201delT|||||4201|WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3134T>C|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,ATAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3135delT|||||3135|WARNING_TRANSCRIPT_NO_START_CODON,ACTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3134T>C|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,ATAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3135delT|||||3135|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:23:20,2,1:20:726:2,1:75,9:-0.312765,0,-58.9375,-5.91932,-59.0435,-64.8871

+NC_045512.2	5869	.	C	A	8.91572E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=24.5973;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.004;PAIRED=1;PAIREDR=0.941176;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=613;RO=17;RPL=1;RPP=5.18177;RPPR=9.26925;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=7;SRP=4.1599;SRR=10;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5604C>A|p.Tyr1868*|5604/21291|5604/21291|1868/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5604C>A|p.Tyr1868*|5604/13218|5604/13218|1868/4405||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3150C>A|p.Tyr1050*|3150/5835|3150/5835|1050/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3150C>A|p.Tyr1050*|3150/5835|3150/5835|1050/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2686C>A|||||2686|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2686C>A|||||2686|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4186C>A|||||4186|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4186C>A|||||4186|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3150C>A|||||3150|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3150C>A|||||3150|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:613:1:38:0,-1.62127,-51.7006

+NC_045512.2	5952	.	T	G	4.17411E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=29.9892;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=746;RO=20;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=3.0103;SRR=10;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5687T>G|p.Leu1896Trp|5687/21291|5687/21291|1896/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5687T>G|p.Leu1896Trp|5687/13218|5687/13218|1896/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3233T>G|p.Leu1078Trp|3233/5835|3233/5835|1078/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3233T>G|p.Leu1078Trp|3233/5835|3233/5835|1078/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2603T>G|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2603T>G|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4103T>G|||||4103|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4103T>G|||||4103|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3233T>G|||||3233|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3233T>G|||||3233|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:746:1:12:0,-5.12164,-66.269

+NC_045512.2	5986	.	C	T	571.853	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=19;CIGAR=1X;DP=19;DPB=19;DPRA=0;EPP=3.12459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=30.9448;PAIRED=0.947368;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=712;QR=0;RO=0;RPL=0;RPP=44.2683;RPPR=0;RPR=19;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721C>T|p.Phe1907Phe|5721/21291|5721/21291|1907/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5721C>T|p.Phe1907Phe|5721/13218|5721/13218|1907/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3267C>T|p.Phe1089Phe|3267/5835|3267/5835|1089/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3267C>T|p.Phe1089Phe|3267/5835|3267/5835|1089/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2569C>T|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2569C>T|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4069C>T|||||4069|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4069C>T|||||4069|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4987C>T|||||4987|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4987C>T|||||4987|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3267C>T|||||3267|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3267C>T|||||3267|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:19:0,19:0:0:19:712:-64.4128,-5.71957,0

+NC_045512.2	6193	.	A	G	4.07431E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1100;RO=29;RPL=1;RPP=5.18177;RPPR=15.6647;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=15.6647;SRR=8;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5928A>G|p.Thr1976Thr|5928/21291|5928/21291|1976/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5928A>G|p.Thr1976Thr|5928/13218|5928/13218|1976/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3474A>G|p.Thr1158Thr|3474/5835|3474/5835|1158/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3474A>G|p.Thr1158Thr|3474/5835|3474/5835|1158/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2362A>G|||||2362|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2362A>G|||||2362|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3862A>G|||||3862|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3862A>G|||||3862|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4780A>G|||||4780|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4780A>G|||||4780|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3474A>G|||||3474|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3474A>G|||||3474|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1100:1:38:0,-5.23363,-95.5115

+NC_045512.2	6241	.	G	T	4.07431E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1085;RO=29;RPL=1;RPP=5.18177;RPPR=15.6647;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=15.6647;SRR=8;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5976G>T|p.Trp1992Cys|5976/21291|5976/21291|1992/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5976G>T|p.Trp1992Cys|5976/13218|5976/13218|1992/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3522G>T|p.Trp1174Cys|3522/5835|3522/5835|1174/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3522G>T|p.Trp1174Cys|3522/5835|3522/5835|1174/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2314G>T|||||2314|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2314G>T|||||2314|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3814G>T|||||3814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3814G>T|||||3814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4732G>T|||||4732|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4732G>T|||||4732|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3522G>T|||||3522|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3522G>T|||||3522|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1085:1:38:0,-5.23363,-94.1611

+NC_045512.2	6250	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=10.8184;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=64.5202;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=21;QR=1680;RO=47;RPL=0;RPP=5.18177;RPPR=41.8658;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=4.16534;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5985C>A|p.Asn1995Lys|5985/21291|5985/21291|1995/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5985C>A|p.Asn1995Lys|5985/13218|5985/13218|1995/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3531C>A|p.Asn1177Lys|3531/5835|3531/5835|1177/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3531C>A|p.Asn1177Lys|3531/5835|3531/5835|1177/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2305C>A|||||2305|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2305C>A|||||2305|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3805C>A|||||3805|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3805C>A|||||3805|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4723C>A|||||4723|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4723C>A|||||4723|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3531C>A|||||3531|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3531C>A|||||3531|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:47,1:47:1680:1:21:0,-12.3495,-149.361

+NC_045512.2	6279	.	C	T	5.28897E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.4488;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1441;RO=40;RPL=0;RPP=7.35324;RPPR=89.8692;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6014C>T|p.Pro2005Leu|6014/21291|6014/21291|2005/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6014C>T|p.Pro2005Leu|6014/13218|6014/13218|2005/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3560C>T|p.Pro1187Leu|3560/5835|3560/5835|1187/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3560C>T|p.Pro1187Leu|3560/5835|3560/5835|1187/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2276C>T|||||2276|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2276C>T|||||2276|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3776C>T|||||3776|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3776C>T|||||3776|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4694C>T|||||4694|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4694C>T|||||4694|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3560C>T|||||3560|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3560C>T|||||3560|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:40,2:40:1441:2:75:0,-5.52292,-122.849

+NC_045512.2	6280	.	A	G	5.28897E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.4488;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1425;RO=40;RPL=0;RPP=7.35324;RPPR=89.8692;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6015A>G|p.Pro2005Pro|6015/21291|6015/21291|2005/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6015A>G|p.Pro2005Pro|6015/13218|6015/13218|2005/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3561A>G|p.Pro1187Pro|3561/5835|3561/5835|1187/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3561A>G|p.Pro1187Pro|3561/5835|3561/5835|1187/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2275A>G|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2275A>G|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3775A>G|||||3775|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3775A>G|||||3775|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4693A>G|||||4693|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4693A>G|||||4693|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3561A>G|||||3561|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3561A>G|||||3561|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:40,2:40:1425:2:75:0,-5.52292,-121.408

+NC_045512.2	6359	.	G	T	2.78774E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9548;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1540;RO=41;RPL=1;RPP=5.18177;RPPR=3.06326;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6094G>T|p.Asp2032Tyr|6094/21291|6094/21291|2032/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6094G>T|p.Asp2032Tyr|6094/13218|6094/13218|2032/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3640G>T|p.Asp1214Tyr|3640/5835|3640/5835|1214/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3640G>T|p.Asp1214Tyr|3640/5835|3640/5835|1214/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2196G>T|||||2196|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2196G>T|||||2196|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3696G>T|||||3696|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3696G>T|||||3696|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4614G>T|||||4614|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4614G>T|||||4614|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3640G>T|||||3640|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3640G>T|||||3640|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1540:1:27:0,-9.94348,-136.18

+NC_045512.2	6433	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=42.2313;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1451;RO=40;RPL=2;RPP=7.35324;RPPR=89.8692;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6168C>T|p.Thr2056Thr|6168/21291|6168/21291|2056/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6168C>T|p.Thr2056Thr|6168/13218|6168/13218|2056/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3714C>T|p.Thr1238Thr|3714/5835|3714/5835|1238/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3714C>T|p.Thr1238Thr|3714/5835|3714/5835|1238/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2122C>T|||||2122|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2122C>T|||||2122|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3622C>T|||||3622|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3622C>T|||||3622|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4540C>T|||||4540|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4540C>T|||||4540|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3714C>T|||||3714|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3714C>T|||||3714|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:40,2:40:1451:2:76:0,-5.42845,-123.655

+NC_045512.2	6439	.	G	T	6.90097E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1502;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6174G>T|p.Gln2058His|6174/21291|6174/21291|2058/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6174G>T|p.Gln2058His|6174/13218|6174/13218|2058/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3720G>T|p.Gln1240His|3720/5835|3720/5835|1240/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3720G>T|p.Gln1240His|3720/5835|3720/5835|1240/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2116G>T|||||2116|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2116G>T|||||2116|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3616G>T|||||3616|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3616G>T|||||3616|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4534G>T|||||4534|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4534G>T|||||4534|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3720G>T|||||3720|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3720G>T|||||3720|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1502:1:11:0,-11.5433,-134.358

+NC_045512.2	6447	.	T	G	1.49216E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.3292;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1457;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6182T>G|p.Val2061Gly|6182/21291|6182/21291|2061/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6182T>G|p.Val2061Gly|6182/13218|6182/13218|2061/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3728T>G|p.Val1243Gly|3728/5835|3728/5835|1243/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3728T>G|p.Val1243Gly|3728/5835|3728/5835|1243/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2108T>G|||||2108|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2108T>G|||||2108|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3608T>G|||||3608|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3608T>G|||||3608|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4526T>G|||||4526|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4526T>G|||||4526|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3728T>G|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3728T>G|||||3728|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1457:1:8:0,-11.8433,-130.607

+NC_045512.2	6455	.	T	G	1.03067E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.5595;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1524;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6190T>G|p.Cys2064Gly|6190/21291|6190/21291|2064/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6190T>G|p.Cys2064Gly|6190/13218|6190/13218|2064/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3736T>G|p.Cys1246Gly|3736/5835|3736/5835|1246/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3736T>G|p.Cys1246Gly|3736/5835|3736/5835|1246/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2100T>G|||||2100|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2100T>G|||||2100|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3600T>G|||||3600|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3600T>G|||||3600|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4518T>G|||||4518|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4518T>G|||||4518|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3736T>G|||||3736|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3736T>G|||||3736|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1524:1:7:0,-11.9433,-136.744

+NC_045512.2	6593	.	C	A	1.37118E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.2645;PAIRED=0;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1475;RO=41;RPL=0;RPP=5.18177;RPPR=92.0407;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6328C>A|p.Pro2110Thr|6328/21291|6328/21291|2110/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6328C>A|p.Pro2110Thr|6328/13218|6328/13218|2110/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3874C>A|p.Pro1292Thr|3874/5835|3874/5835|1292/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3874C>A|p.Pro1292Thr|3874/5835|3874/5835|1292/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1962C>A|||||1962|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1962C>A|||||1962|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3462C>A|||||3462|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3462C>A|||||3462|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4380C>A|||||4380|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4380C>A|||||4380|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3874C>A|||||3874|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3874C>A|||||3874|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1475:1:30:0,-9.64369,-130.032

+NC_045512.2	6643	.	T	C	6.90097E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=92.0407;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1540;RO=41;RPL=1;RPP=5.18177;RPPR=3.48696;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.48696;SRR=22;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6378T>C|p.Gly2126Gly|6378/21291|6378/21291|2126/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6378T>C|p.Gly2126Gly|6378/13218|6378/13218|2126/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3924T>C|p.Gly1308Gly|3924/5835|3924/5835|1308/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3924T>C|p.Gly1308Gly|3924/5835|3924/5835|1308/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1912T>C|||||1912|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1912T>C|||||1912|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3412T>C|||||3412|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3412T>C|||||3412|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4330T>C|||||4330|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4330T>C|||||4330|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3924T>C|||||3924|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3924T>C|||||3924|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1540:1:11:0,-11.5433,-137.782

+NC_045512.2	6722	.	A	C,T	1.28098E-15	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=1,1;CIGAR=1X,1X;DP=42;DPB=42;DPRA=0,0;EPP=5.18177,5.18177;EPPR=29.2851;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=57.518;PAIRED=0,1;PAIREDR=0.975;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=11,10;QR=1508;RO=40;RPL=0,1;RPP=5.18177,5.18177;RPPR=16.9077;RPR=1,0;RUN=1,1;SAF=0,1;SAP=5.18177,5.18177;SAR=1,0;SRF=19;SRP=3.22745;SRR=21;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6457A>C|p.Thr2153Pro|6457/21291|6457/21291|2153/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6457A>T|p.Thr2153Ser|6457/21291|6457/21291|2153/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6457A>C|p.Thr2153Pro|6457/13218|6457/13218|2153/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6457A>T|p.Thr2153Ser|6457/13218|6457/13218|2153/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4003A>C|p.Thr1335Pro|4003/5835|4003/5835|1335/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4003A>T|p.Thr1335Ser|4003/5835|4003/5835|1335/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4003A>C|p.Thr1335Pro|4003/5835|4003/5835|1335/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4003A>T|p.Thr1335Ser|4003/5835|4003/5835|1335/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1833A>C|||||1833|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1833A>T|||||1833|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1833A>C|||||1833|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1833A>T|||||1833|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3333A>C|||||3333|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3333A>T|||||3333|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3333A>C|||||3333|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3333A>T|||||3333|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4251A>C|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4251A>T|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4251A>C|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4251A>T|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4003A>C|||||4003|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4003A>T|||||4003|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4003A>C|||||4003|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4003A>T|||||4003|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:40,1,1:40:1508:1,1:11,10:0,-11.3472,-134.903,-11.4472,-134.611,-134.993

+NC_045512.2	6742	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.4278;PAIRED=0;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1504;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6477G>A|p.Arg2159Arg|6477/21291|6477/21291|2159/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6477G>A|p.Arg2159Arg|6477/13218|6477/13218|2159/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4023G>A|p.Arg1341Arg|4023/5835|4023/5835|1341/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4023G>A|p.Arg1341Arg|4023/5835|4023/5835|1341/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1813G>A|||||1813|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1813G>A|||||1813|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3313G>A|||||3313|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3313G>A|||||3313|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4231G>A|||||4231|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4231G>A|||||4231|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4023G>A|||||4023|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4023G>A|||||4023|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1504:1:38:0,-8.84599,-131.839

+NC_045512.2	6744	.	GTTTA	ATTTT	2.78774E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=54.9548;PAIRED=0;PAIREDR=0.97561;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1521;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=complex;ANN=ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6479_6483delGTTTAinsATTTT|p.CysLeu2160TyrPhe|6479/21291|6479/21291|2160/7096||,ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6479_6483delGTTTAinsATTTT|p.CysLeu2160TyrPhe|6479/13218|6479/13218|2160/4405||,ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4025_4029delGTTTAinsATTTT|p.CysLeu1342TyrPhe|4025/5835|4025/5835|1342/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4025_4029delGTTTAinsATTTT|p.CysLeu1342TyrPhe|4025/5835|4025/5835|1342/1944||WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1811_-1807delGTTTAinsATTTT|||||1811|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1811_-1807delGTTTAinsATTTT|||||1811|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3311_-3307delGTTTAinsATTTT|||||3311|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3311_-3307delGTTTAinsATTTT|||||3311|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4229_-4225delGTTTAinsATTTT|||||4229|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4229_-4225delGTTTAinsATTTT|||||4229|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4025_*4029delGTTTAinsATTTT|||||4025|WARNING_TRANSCRIPT_NO_START_CODON,ATTTT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4025_*4029delGTTTAinsATTTT|||||4025|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1521:1:27:0,-9.94348,-134.474

+NC_045512.2	6762	.	C	A	6.90097E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.6385;PAIRED=1;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1505;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6497C>A|p.Thr2166Asn|6497/21291|6497/21291|2166/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6497C>A|p.Thr2166Asn|6497/13218|6497/13218|2166/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4043C>A|p.Thr1348Asn|4043/5835|4043/5835|1348/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4043C>A|p.Thr1348Asn|4043/5835|4043/5835|1348/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1793C>A|||||1793|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1793C>A|||||1793|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3293C>A|||||3293|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3293C>A|||||3293|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4211C>A|||||4211|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4211C>A|||||4211|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4043C>A|||||4043|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4043C>A|||||4043|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1505:1:11:0,-11.5433,-134.631

+NC_045512.2	6828	.	C	T	1.7035E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=26.2658;PAIRED=1;PAIREDR=0.904762;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=797;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=48.6112;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6563C>T|p.Ser2188Phe|6563/21291|6563/21291|2188/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6563C>T|p.Ser2188Phe|6563/13218|6563/13218|2188/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4109C>T|p.Ser1370Phe|4109/5835|4109/5835|1370/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4109C>T|p.Ser1370Phe|4109/5835|4109/5835|1370/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1727C>T|||||1727|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1727C>T|||||1727|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3227C>T|||||3227|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3227C>T|||||3227|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4145C>T|||||4145|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4145C>T|||||4145|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4109C>T|||||4109|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4109C>T|||||4109|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:797:1:34:0,-3.22375,-68.6592

+NC_045512.2	6839	.	G	T	9.29677E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=48.6112;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5592;PAIRED=0;PAIREDR=0.952381;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=783;RO=21;RPL=1;RPP=5.18177;RPPR=48.6112;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=48.6112;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6574G>T|p.Ala2192Ser|6574/21291|6574/21291|2192/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6574G>T|p.Ala2192Ser|6574/13218|6574/13218|2192/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4120G>T|p.Ala1374Ser|4120/5835|4120/5835|1374/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4120G>T|p.Ala1374Ser|4120/5835|4120/5835|1374/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1716G>T|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1716G>T|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3216G>T|||||3216|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3216G>T|||||3216|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4134G>T|||||4134|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4134G>T|||||4134|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4120G>T|||||4120|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4120G>T|||||4120|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:783:1:11:0,-5.52266,-69.6938

+NC_045512.2	7975	.	G	A	1.77522E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=31.2394;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7101;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=493;RO=13;RPL=0;RPP=5.18177;RPPR=31.2394;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=31.2394;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7710G>A|p.Leu2570Leu|7710/21291|7710/21291|2570/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7710G>A|p.Leu2570Leu|7710/13218|7710/13218|2570/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5256G>A|p.Leu1752Leu|5256/5835|5256/5835|1752/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5256G>A|p.Leu1752Leu|5256/5835|5256/5835|1752/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-580G>A|||||580|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-580G>A|||||580|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2080G>A|||||2080|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2080G>A|||||2080|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2998G>A|||||2998|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2998G>A|||||2998|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3868G>A|||||3868|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3868G>A|||||3868|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4117G>A|||||4117|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4117G>A|||||4117|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4711G>A|||||4711|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4711G>A|||||4711|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:14:13,1:13:493:1:38:0,-0.417151,-40.9202

+NC_045512.2	8252	.	A	C	5.07863E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.5668;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=562;RO=15;RPL=0;RPP=5.18177;RPPR=20.5268;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=20.5268;SRR=13;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7987A>C|p.Ile2663Leu|7987/21291|7987/21291|2663/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7987A>C|p.Ile2663Leu|7987/13218|7987/13218|2663/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5533A>C|p.Ile1845Leu|5533/5835|5533/5835|1845/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5533A>C|p.Ile1845Leu|5533/5835|5533/5835|1845/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-303A>C|||||303|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-303A>C|||||303|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1803A>C|||||1803|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1803A>C|||||1803|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2721A>C|||||2721|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2721A>C|||||2721|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3591A>C|||||3591|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3591A>C|||||3591|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3840A>C|||||3840|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3840A>C|||||3840|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4434A>C|||||4434|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4434A>C|||||4434|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4773A>C|||||4773|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4773A>C|||||4773|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:562:1:24:0,-2.41659,-48.5206

+NC_045512.2	8254	.	AGA	AA	5.06717E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=16;DPB=15.6667;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.2665;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=564;RO=15;RPL=0;RPP=5.18177;RPPR=20.5268;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=20.5268;SRR=13;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7990delG|p.Glu2664fs|7990/21291|7990/21291|2664/7096||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7990delG|p.Glu2664fs|7990/13218|7990/13218|2664/4405||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5536delG|p.Glu1846fs|5536/5835|5536/5835|1846/1944||WARNING_TRANSCRIPT_NO_START_CODON,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5536delG|p.Glu1846fs|5536/5835|5536/5835|1846/1944||WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-300delG|||||300|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-300delG|||||300|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1800delG|||||1800|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1800delG|||||1800|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2718delG|||||2718|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2718delG|||||2718|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3588delG|||||3588|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3588delG|||||3588|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3837delG|||||3837|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3837delG|||||3837|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4431delG|||||4431|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4431delG|||||4431|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4770delG|||||4770|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4770delG|||||4770|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:564:1:34:0,-1.41757,-47.7023

+NC_045512.2	8335	.	T	G	1.26801E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=16;DPB=16;DPRA=0;EPP=5.18177;EPPR=35.5824;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=17.3492;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=550;RO=15;RPL=0;RPP=5.18177;RPPR=10.1038;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=10.1038;SRR=11;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8070T>G|p.Ala2690Ala|8070/21291|8070/21291|2690/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8070T>G|p.Ala2690Ala|8070/13218|8070/13218|2690/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5616T>G|p.Ala1872Ala|5616/5835|5616/5835|1872/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5616T>G|p.Ala1872Ala|5616/5835|5616/5835|1872/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-220T>G|||||220|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-220T>G|||||220|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1720T>G|||||1720|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1720T>G|||||1720|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2638T>G|||||2638|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2638T>G|||||2638|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3508T>G|||||3508|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3508T>G|||||3508|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3757T>G|||||3757|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3757T>G|||||3757|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4351T>G|||||4351|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4351T>G|||||4351|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4690T>G|||||4690|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4690T>G|||||4690|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:16:15,1:15:550:1:38:0,-1.01921,-46.0397

+NC_045512.2	8339	.	A	T	1.66407E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=13;DPB=13;DPRA=0;EPP=5.18177;EPPR=29.068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7748;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32;QR=426;RO=12;RPL=1;RPP=5.18177;RPPR=3.73412;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.73412;SRR=7;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8074A>T|p.Ile2692Phe|8074/21291|8074/21291|2692/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8074A>T|p.Ile2692Phe|8074/13218|8074/13218|2692/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5620A>T|p.Ile1874Phe|5620/5835|5620/5835|1874/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5620A>T|p.Ile1874Phe|5620/5835|5620/5835|1874/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-216A>T|||||216|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-216A>T|||||216|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1716A>T|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1716A>T|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2634A>T|||||2634|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2634A>T|||||2634|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3504A>T|||||3504|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3504A>T|||||3504|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3753A>T|||||3753|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3753A>T|||||3753|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4347A>T|||||4347|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4347A>T|||||4347|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4686A>T|||||4686|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4686A>T|||||4686|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:13:12,1:12:426:1:32:0,-0.714077,-35.4767

+NC_045512.2	8340	.	T	G	6.15389E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=18.0721;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=392;RO=11;RPL=1;RPP=5.18177;RPPR=3.20771;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=3.20771;SRR=6;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8075T>G|p.Ile2692Ser|8075/21291|8075/21291|2692/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8075T>G|p.Ile2692Ser|8075/13218|8075/13218|2692/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5621T>G|p.Ile1874Ser|5621/5835|5621/5835|1874/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5621T>G|p.Ile1874Ser|5621/5835|5621/5835|1874/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-215T>G|||||215|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-215T>G|||||215|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1715T>G|||||1715|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1715T>G|||||1715|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2633T>G|||||2633|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2633T>G|||||2633|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3503T>G|||||3503|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3503T>G|||||3503|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3752T>G|||||3752|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3752T>G|||||3752|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4346T>G|||||4346|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4346T>G|||||4346|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4685T>G|||||4685|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4685T>G|||||4685|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:12:11,1:11:392:1:12:0,-2.41237,-34.4184

+NC_045512.2	8375	.	G	T	0.293568	.	AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=3.0103;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.66021;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=302;RO=9;RPL=0;RPP=7.35324;RPPR=22.5536;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8110G>T|p.Ala2704Ser|8110/21291|8110/21291|2704/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8110G>T|p.Ala2704Ser|8110/13218|8110/13218|2704/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5656G>T|p.Ala1886Ser|5656/5835|5656/5835|1886/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5656G>T|p.Ala1886Ser|5656/5835|5656/5835|1886/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-180G>T|||||180|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-180G>T|||||180|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1680G>T|||||1680|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1680G>T|||||1680|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2598G>T|||||2598|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2598G>T|||||2598|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3468G>T|||||3468|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3468G>T|||||3468|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3717G>T|||||3717|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3717G>T|||||3717|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4311G>T|||||4311|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4311G>T|||||4311|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4650G>T|||||4650|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4650G>T|||||4650|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:9,2:9:302:2:73:-3.61977,0,-24.1879

+NC_045512.2	8480	.	C	T	0.547656	.	AB=0.181818;ABP=12.6832;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=11;DPB=11;DPRA=0;EPP=7.35324;EPPR=22.5536;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2.00695;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=337;RO=9;RPL=1;RPP=3.0103;RPPR=3.25157;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8215C>T|p.Pro2739Ser|8215/21291|8215/21291|2739/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8215C>T|p.Pro2739Ser|8215/13218|8215/13218|2739/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5761C>T|p.Pro1921Ser|5761/5835|5761/5835|1921/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5761C>T|p.Pro1921Ser|5761/5835|5761/5835|1921/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-75C>T|||||75|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-75C>T|||||75|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1575C>T|||||1575|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1575C>T|||||1575|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2493C>T|||||2493|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2493C>T|||||2493|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3363C>T|||||3363|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3363C>T|||||3363|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3612C>T|||||3612|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3612C>T|||||3612|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4206C>T|||||4206|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4206C>T|||||4206|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4545C>T|||||4545|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4545C>T|||||4545|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4962C>T|||||4962|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4962C>T|||||4962|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:11:9,2:9:337:2:76:-3.90348,0,-27.3727

+NC_045512.2	8656	.	T	C	1.2603E-4	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=5.18177;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=10.4475;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=190;RO=5;RPL=1;RPP=5.18177;RPPR=13.8677;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=13.8677;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8391T>C|p.Ser2797Ser|8391/21291|8391/21291|2797/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8391T>C|p.Ser2797Ser|8391/13218|8391/13218|2797/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.102T>C|p.Ser34Ser|102/1500|102/1500|34/499||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.102T>C|p.Ser34Ser|102/1500|102/1500|34/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1399T>C|||||1399|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1399T>C|||||1399|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2317T>C|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2317T>C|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3187T>C|||||3187|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3187T>C|||||3187|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3436T>C|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3436T>C|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4030T>C|||||4030|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4030T>C|||||4030|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4369T>C|||||4369|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4369T>C|||||4369|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4786T>C|||||4786|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4786T>C|||||4786|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*102T>C|||||102|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*102T>C|||||102|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:6:5,1:5:190:1:12:0,-0.606186,-16.2674

+NC_045512.2	8891	.	A	C	9.75095E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=15.3093;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24;QR=352;RO=11;RPL=0;RPP=5.18177;RPPR=26.8965;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=26.8965;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8626A>C|p.Thr2876Pro|8626/21291|8626/21291|2876/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8626A>C|p.Thr2876Pro|8626/13218|8626/13218|2876/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.337A>C|p.Thr113Pro|337/1500|337/1500|113/499||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.337A>C|p.Thr113Pro|337/1500|337/1500|113/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1164A>C|||||1164|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1164A>C|||||1164|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2082A>C|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2082A>C|||||2082|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2952A>C|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2952A>C|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3201A>C|||||3201|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3201A>C|||||3201|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3795A>C|||||3795|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3795A>C|||||3795|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4134A>C|||||4134|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4134A>C|||||4134|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4551A>C|||||4551|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4551A>C|||||4551|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*337A>C|||||337|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*337A>C|||||337|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:12:11,1:11:352:1:24:0,-1.21247,-29.5902

+NC_045512.2	8897	.	A	T	3.56285E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=39.9253;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9213;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=633;RO=17;RPL=0;RPP=5.18177;RPPR=39.9253;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=39.9253;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8632A>T|p.Asn2878Tyr|8632/21291|8632/21291|2878/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8632A>T|p.Asn2878Tyr|8632/13218|8632/13218|2878/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.343A>T|p.Asn115Tyr|343/1500|343/1500|115/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.343A>T|p.Asn115Tyr|343/1500|343/1500|115/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1158A>T|||||1158|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1158A>T|||||1158|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2076A>T|||||2076|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2076A>T|||||2076|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2946A>T|||||2946|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2946A>T|||||2946|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3195A>T|||||3195|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3195A>T|||||3195|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3789A>T|||||3789|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3789A>T|||||3789|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4128A>T|||||4128|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4128A>T|||||4128|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4545A>T|||||4545|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4545A>T|||||4545|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*343A>T|||||343|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*343A>T|||||343|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:633:1:34:0,-2.01963,-53.9064

+NC_045512.2	8966	.	A	G	9.29677E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=5.18177;EPPR=20.4855;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=31.5592;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=789;RO=21;RPL=0;RPP=5.18177;RPPR=48.6112;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=20.4855;SRR=4;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8701A>G|p.Lys2901Glu|8701/21291|8701/21291|2901/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8701A>G|p.Lys2901Glu|8701/13218|8701/13218|2901/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.412A>G|p.Lys138Glu|412/1500|412/1500|138/499||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.412A>G|p.Lys138Glu|412/1500|412/1500|138/499||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1089A>G|||||1089|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1089A>G|||||1089|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2007A>G|||||2007|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2007A>G|||||2007|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2877A>G|||||2877|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2877A>G|||||2877|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3126A>G|||||3126|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3126A>G|||||3126|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3720A>G|||||3720|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3720A>G|||||3720|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4059A>G|||||4059|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4059A>G|||||4059|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4476A>G|||||4476|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4476A>G|||||4476|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*412A>G|||||412|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*412A>G|||||412|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:22:21,1:21:789:1:11:0,-5.52266,-70.2371

+NC_045512.2	8975	.	G	T	2.27069E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1894;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=1245;RO=34;RPL=0;RPP=7.35324;RPPR=76.8404;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8710G>T|p.Glu2904*|8710/21291|8710/21291|2904/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8710G>T|p.Glu2904*|8710/13218|8710/13218|2904/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.421G>T|p.Glu141*|421/1500|421/1500|141/499||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.421G>T|p.Glu141*|421/1500|421/1500|141/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1080G>T|||||1080|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1080G>T|||||1080|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1998G>T|||||1998|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1998G>T|||||1998|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2868G>T|||||2868|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2868G>T|||||2868|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3117G>T|||||3117|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3117G>T|||||3117|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3711G>T|||||3711|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3711G>T|||||3711|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4050G>T|||||4050|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4050G>T|||||4050|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4467G>T|||||4467|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4467G>T|||||4467|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*421G>T|||||421|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*421G>T|||||421|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,2:34:1245:2:67:0,-4.475,-105.982

+NC_045512.2	8991	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=3.07234;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.9354;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1296;RO=35;RPL=0;RPP=5.18177;RPPR=79.0118;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8726C>A|p.Ala2909Glu|8726/21291|8726/21291|2909/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8726C>A|p.Ala2909Glu|8726/13218|8726/13218|2909/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.437C>A|p.Ala146Glu|437/1500|437/1500|146/499||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.437C>A|p.Ala146Glu|437/1500|437/1500|146/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1064C>A|||||1064|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1064C>A|||||1064|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1982C>A|||||1982|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1982C>A|||||1982|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2852C>A|||||2852|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2852C>A|||||2852|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3101C>A|||||3101|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3101C>A|||||3101|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3695C>A|||||3695|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3695C>A|||||3695|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4034C>A|||||4034|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4034C>A|||||4034|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4451C>A|||||4451|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4451C>A|||||4451|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*437C>A|||||437|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*437C>A|||||437|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1296:1:9:0,-9.93708,-116.035

+NC_045512.2	9041	.	T	C	2.59963E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=48.239;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.1814;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1308;RO=35;RPL=0;RPP=5.18177;RPPR=8.03571;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=3.07234;SRR=18;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8776T>C|p.Ser2926Pro|8776/21291|8776/21291|2926/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8776T>C|p.Ser2926Pro|8776/13218|8776/13218|2926/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.487T>C|p.Ser163Pro|487/1500|487/1500|163/499||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.487T>C|p.Ser163Pro|487/1500|487/1500|163/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1014T>C|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1014T>C|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1932T>C|||||1932|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1932T>C|||||1932|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2802T>C|||||2802|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2802T>C|||||2802|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3051T>C|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3051T>C|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3645T>C|||||3645|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3645T>C|||||3645|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3984T>C|||||3984|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3984T>C|||||3984|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4401T>C|||||4401|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4401T>C|||||4401|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*487T>C|||||487|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*487T>C|||||487|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1308:1:34:0,-7.43817,-114.613

+NC_045512.2	9049	.	G	T	1.87615E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.4749;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1309;RO=35;RPL=0;RPP=5.18177;RPPR=3.07234;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=18;SRP=3.07234;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8784G>T|p.Lys2928Asn|8784/21291|8784/21291|2928/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8784G>T|p.Lys2928Asn|8784/13218|8784/13218|2928/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.495G>T|p.Lys165Asn|495/1500|495/1500|165/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.495G>T|p.Lys165Asn|495/1500|495/1500|165/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1006G>T|||||1006|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1006G>T|||||1006|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1924G>T|||||1924|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1924G>T|||||1924|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2794G>T|||||2794|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2794G>T|||||2794|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3043G>T|||||3043|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3043G>T|||||3043|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3637G>T|||||3637|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3637G>T|||||3637|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3976G>T|||||3976|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3976G>T|||||3976|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4393G>T|||||4393|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4393G>T|||||4393|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*495G>T|||||495|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*495G>T|||||495|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1309:1:11:0,-9.73708,-117.004

+NC_045512.2	9123	.	G	C	3.26967E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2259;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1286;RO=34;RPL=2;RPP=7.35324;RPPR=76.8404;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=17;SRP=3.0103;SRR=17;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8858G>C|p.Arg2953Pro|8858/21291|8858/21291|2953/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8858G>C|p.Arg2953Pro|8858/13218|8858/13218|2953/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.569G>C|p.Arg190Pro|569/1500|569/1500|190/499||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.569G>C|p.Arg190Pro|569/1500|569/1500|190/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-932G>C|||||932|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-932G>C|||||932|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1850G>C|||||1850|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1850G>C|||||1850|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2720G>C|||||2720|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2720G>C|||||2720|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2969G>C|||||2969|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2969G>C|||||2969|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3563G>C|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3563G>C|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3902G>C|||||3902|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3902G>C|||||3902|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4319G>C|||||4319|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4319G>C|||||4319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*569G>C|||||569|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*569G>C|||||569|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:34,2:34:1286:2:76:0,-3.62227,-108.822

+NC_045512.2	9269	.	G	T	9.72896E-6	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=12;DPB=12;DPRA=0;EPP=5.18177;EPPR=26.8965;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=13.009;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=382;RO=11;RPL=1;RPP=5.18177;RPPR=12.6832;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=2;SRP=12.6832;SRR=9;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9004G>T|p.Gly3002Cys|9004/21291|9004/21291|3002/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9004G>T|p.Gly3002Cys|9004/13218|9004/13218|3002/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.715G>T|p.Gly239Cys|715/1500|715/1500|239/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.715G>T|p.Gly239Cys|715/1500|715/1500|239/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-786G>T|||||786|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-786G>T|||||786|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1704G>T|||||1704|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1704G>T|||||1704|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2574G>T|||||2574|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2574G>T|||||2574|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2823G>T|||||2823|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2823G>T|||||2823|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3417G>T|||||3417|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3417G>T|||||3417|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3756G>T|||||3756|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3756G>T|||||3756|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4173G>T|||||4173|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4173G>T|||||4173|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*715G>T|||||715|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*715G>T|||||715|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:12:11,1:11:382:1:34:0,-0.213449,-31.3145

+NC_045512.2	10040	.	T	C	4.11236E-7	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=5.18177;EPPR=3.25157;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=16.1727;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=297;RO=9;RPL=1;RPP=5.18177;RPPR=22.5536;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=4;SRP=3.25157;SRR=5;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9775T>C|p.Ser3259Pro|9775/21291|9775/21291|3259/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9775T>C|p.Ser3259Pro|9775/13218|9775/13218|3259/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1486T>C|p.Ser496Pro|1486/1500|1486/1500|496/499||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1486T>C|p.Ser496Pro|1486/1500|1486/1500|496/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-15T>C|||||15|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-15T>C|||||15|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-933T>C|||||933|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-933T>C|||||933|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1803T>C|||||1803|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1803T>C|||||1803|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2052T>C|||||2052|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2052T>C|||||2052|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2646T>C|||||2646|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2646T>C|||||2646|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2985T>C|||||2985|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2985T>C|||||2985|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3402T>C|||||3402|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3402T>C|||||3402|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1486T>C|||||1486|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1486T>C|||||1486|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:10:9,1:9:297:1:9:0,-2.1103,-26.1442

+NC_045512.2	10168	.	T	G	1.04727E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=60;DPB=60;DPRA=0;EPP=5.18177;EPPR=5.99147;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=83.0048;PAIRED=1;PAIREDR=0.779661;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=2057;RO=59;RPL=1;RPP=5.18177;RPPR=98.7391;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=30;SRP=3.0471;SRR=29;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9903T>G|p.Cys3301Trp|9903/21291|9903/21291|3301/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9903T>G|p.Cys3301Trp|9903/13218|9903/13218|3301/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.114T>G|p.Cys38Trp|114/918|114/918|38/305||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.114T>G|p.Cys38Trp|114/918|114/918|38/305||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-805T>G|||||805|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-805T>G|||||805|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1675T>G|||||1675|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1675T>G|||||1675|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1924T>G|||||1924|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1924T>G|||||1924|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2518T>G|||||2518|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2518T>G|||||2518|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2857T>G|||||2857|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2857T>G|||||2857|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3274T>G|||||3274|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3274T>G|||||3274|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1614T>G|||||1614|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1614T>G|||||1614|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*114T>G|||||114|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*114T>G|||||114|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:60:59,1:59:2057:1:12:0,-16.8618,-184.171

+NC_045512.2	10169	.	CCAAG	CG,CTAAG,CCGAG	1.54596E-14	.	AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=2,1,2;CIGAR=1M3D1M,1M1X3M,2M1X2M;DP=55;DPB=56;DPRA=0,0,0;EPP=3.0103,5.18177,3.0103;EPPR=3.70517;GTI=0;LEN=3,1,1;MEANALT=3,3,3;MQM=60,60,60;MQMR=60;NS=1;NUMALT=3;ODDS=56.5225;PAIRED=1,0,1;PAIREDR=0.76;PAO=0.25,0.25,1.25;PQA=8.5,8.5,42.5;PQR=110.5;PRO=3.25;QA=67,27,76;QR=1794;RO=50;RPL=0,0,0;RPP=7.35324,5.18177,7.35324;RPPR=111.584;RPR=2,1,2;RUN=1,1,1;SAF=1,1,1;SAP=3.0103,5.18177,3.0103;SAR=1,0,1;SRF=27;SRP=3.70517;SRR=23;TYPE=del,snp,snp;ANN=CTAAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9905C>T|p.Pro3302Leu|9905/21291|9905/21291|3302/7096||,CTAAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9905C>T|p.Pro3302Leu|9905/13218|9905/13218|3302/4405||,CTAAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.116C>T|p.Pro39Leu|116/918|116/918|39/305||WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.116C>T|p.Pro39Leu|116/918|116/918|39/305||WARNING_TRANSCRIPT_NO_START_CODON,CG|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9905_9907delCAA|p.Pro3302del|9905/21291|9905/21291|3302/7096||,CG|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9905_9907delCAA|p.Pro3302del|9905/13218|9905/13218|3302/4405||,CG|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.116_118delCAA|p.Pro39del|116/918|116/918|39/305||WARNING_TRANSCRIPT_NO_START_CODON,CG|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.116_118delCAA|p.Pro39del|116/918|116/918|39/305||WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9906A>G|p.Pro3302Pro|9906/21291|9906/21291|3302/7096||,CCGAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9906A>G|p.Pro3302Pro|9906/13218|9906/13218|3302/4405||,CCGAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.117A>G|p.Pro39Pro|117/918|117/918|39/305||WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.117A>G|p.Pro39Pro|117/918|117/918|39/305||WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-803C>T|||||803|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-803_-801delCAA|||||803|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-802A>G|||||802|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-803C>T|||||803|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-803_-801delCAA|||||803|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-802A>G|||||802|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1673C>T|||||1673|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1673_-1671delCAA|||||1673|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1672A>G|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1673C>T|||||1673|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1673_-1671delCAA|||||1673|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1672A>G|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1922C>T|||||1922|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1922_-1920delCAA|||||1922|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1921A>G|||||1921|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1922C>T|||||1922|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1922_-1920delCAA|||||1922|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1921A>G|||||1921|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2516C>T|||||2516|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2516_-2514delCAA|||||2516|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2515A>G|||||2515|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2516C>T|||||2516|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2516_-2514delCAA|||||2516|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2515A>G|||||2515|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2855C>T|||||2855|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2855_-2853delCAA|||||2855|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2854A>G|||||2854|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2855C>T|||||2855|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2855_-2853delCAA|||||2855|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2854A>G|||||2854|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3272C>T|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3272_-3270delCAA|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3271A>G|||||3271|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3272C>T|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,CG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3272_-3270delCAA|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3271A>G|||||3271|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1616C>T|||||1616|WARNING_TRANSCRIPT_NO_START_CODON,CG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1616_*1618delCAA|||||1616|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1617A>G|||||1617|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1616C>T|||||1616|WARNING_TRANSCRIPT_NO_START_CODON,CG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1616_*1618delCAA|||||1616|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1617A>G|||||1617|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*116C>T|||||116|WARNING_TRANSCRIPT_NO_START_CODON,CG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*116_*118delCAA|||||116|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*117A>G|||||117|WARNING_TRANSCRIPT_NO_START_CODON,CTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*116C>T|||||116|WARNING_TRANSCRIPT_NO_START_CODON,CG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*116_*118delCAA|||||116|WARNING_TRANSCRIPT_NO_START_CODON,CCGAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*117A>G|||||117|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:50,2,1,2:50:1794:2,1,2:67,27,76:0,-9.63806,-155.337,-12.9384,-153.812,-158.935,-8.81225,-149.705,-153.002,-154.527

+NC_045512.2	10282	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=111.745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=71.7867;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1943;RO=54;RPL=1;RPP=5.18177;RPPR=3.17115;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10017G>T|p.Arg3339Ser|10017/21291|10017/21291|3339/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10017G>T|p.Arg3339Ser|10017/13218|10017/13218|3339/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.228G>T|p.Arg76Ser|228/918|228/918|76/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.228G>T|p.Arg76Ser|228/918|228/918|76/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-691G>T|||||691|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-691G>T|||||691|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1561G>T|||||1561|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1561G>T|||||1561|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1810G>T|||||1810|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1810G>T|||||1810|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2404G>T|||||2404|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2404G>T|||||2404|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2743G>T|||||2743|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2743G>T|||||2743|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3160G>T|||||3160|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3160G>T|||||3160|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1728G>T|||||1728|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1728G>T|||||1728|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*228G>T|||||228|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*228G>T|||||228|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:1943:1:31:0,-13.4572,-172.017

+NC_045512.2	10300	.	GCAA	TCAC	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=111.745;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.3184;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=20;QR=2010;RO=54;RPL=1;RPP=5.18177;RPPR=3.17115;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=complex;ANN=TCAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10035_10038delGCAAinsTCAC|p.MetGln3345IleHis|10035/21291|10035/21291|3345/7096||,TCAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10035_10038delGCAAinsTCAC|p.MetGln3345IleHis|10035/13218|10035/13218|3345/4405||,TCAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.246_249delGCAAinsTCAC|p.MetGln82IleHis|246/918|246/918|82/305||WARNING_TRANSCRIPT_NO_START_CODON,TCAC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.246_249delGCAAinsTCAC|p.MetGln82IleHis|246/918|246/918|82/305||WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-673_-670delGCAAinsTCAC|||||673|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-673_-670delGCAAinsTCAC|||||673|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1543_-1540delGCAAinsTCAC|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1543_-1540delGCAAinsTCAC|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1792_-1789delGCAAinsTCAC|||||1792|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1792_-1789delGCAAinsTCAC|||||1792|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2386_-2383delGCAAinsTCAC|||||2386|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2386_-2383delGCAAinsTCAC|||||2386|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2725_-2722delGCAAinsTCAC|||||2725|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2725_-2722delGCAAinsTCAC|||||2725|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3142_-3139delGCAAinsTCAC|||||3142|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3142_-3139delGCAAinsTCAC|||||3142|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1746_*1749delGCAAinsTCAC|||||1746|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1746_*1749delGCAAinsTCAC|||||1746|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*246_*249delGCAAinsTCAC|||||246|WARNING_TRANSCRIPT_NO_START_CODON,TCAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*246_*249delGCAAinsTCAC|||||246|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:2010:1:20:0,-14.5567,-179.154

+NC_045512.2	10314	.	T	A	4.92735E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=3.0103;EPPR=4.03458;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.7081;PAIRED=1;PAIREDR=0.754717;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1976;RO=53;RPL=2;RPP=7.35324;RPPR=118.098;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=29;SRP=4.03458;SRR=24;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10049T>A|p.Leu3350His|10049/21291|10049/21291|3350/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10049T>A|p.Leu3350His|10049/13218|10049/13218|3350/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.260T>A|p.Leu87His|260/918|260/918|87/305||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.260T>A|p.Leu87His|260/918|260/918|87/305||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-659T>A|||||659|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-659T>A|||||659|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1529T>A|||||1529|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1529T>A|||||1529|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1778T>A|||||1778|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1778T>A|||||1778|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2372T>A|||||2372|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2372T>A|||||2372|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2711T>A|||||2711|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2711T>A|||||2711|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3128T>A|||||3128|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3128T>A|||||3128|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1760T>A|||||1760|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1760T>A|||||1760|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*260T>A|||||260|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*260T>A|||||260|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:53,2:53:1976:2:76:0,-9.34184,-170.875

+NC_045512.2	10323	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2005;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10058A>C|p.Lys3353Thr|10058/21291|10058/21291|3353/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10058A>C|p.Lys3353Thr|10058/13218|10058/13218|3353/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.269A>C|p.Lys90Thr|269/918|269/918|90/305||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.269A>C|p.Lys90Thr|269/918|269/918|90/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-650A>C|||||650|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-650A>C|||||650|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1520A>C|||||1520|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1520A>C|||||1520|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1769A>C|||||1769|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1769A>C|||||1769|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2363A>C|||||2363|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2363A>C|||||2363|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2702A>C|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2702A>C|||||2702|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3119A>C|||||3119|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3119A>C|||||3119|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1769A>C|||||1769|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1769A>C|||||1769|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*269A>C|||||269|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*269A>C|||||269|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:2005:1:9:0,-15.6567,-179.804

+NC_045512.2	10335	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6277;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=1968;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10070C>A|p.Ala3357Asp|10070/21291|10070/21291|3357/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10070C>A|p.Ala3357Asp|10070/13218|10070/13218|3357/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.281C>A|p.Ala94Asp|281/918|281/918|94/305||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.281C>A|p.Ala94Asp|281/918|281/918|94/305||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-638C>A|||||638|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-638C>A|||||638|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1508C>A|||||1508|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1508C>A|||||1508|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1757C>A|||||1757|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1757C>A|||||1757|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2351C>A|||||2351|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2351C>A|||||2351|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2690C>A|||||2690|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2690C>A|||||2690|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3107C>A|||||3107|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3107C>A|||||3107|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1781C>A|||||1781|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1781C>A|||||1781|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*281C>A|||||281|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*281C>A|||||281|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:1968:1:23:0,-14.2567,-175.07

+NC_045512.2	10344	.	A	C	1.28079E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=75.4696;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=15;QR=1964;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10079A>C|p.Lys3360Thr|10079/21291|10079/21291|3360/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10079A>C|p.Lys3360Thr|10079/13218|10079/13218|3360/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.290A>C|p.Lys97Thr|290/918|290/918|97/305||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.290A>C|p.Lys97Thr|290/918|290/918|97/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-629A>C|||||629|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-629A>C|||||629|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1499A>C|||||1499|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1499A>C|||||1499|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1748A>C|||||1748|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1748A>C|||||1748|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2342A>C|||||2342|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2342A>C|||||2342|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2681A>C|||||2681|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2681A>C|||||2681|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3098A>C|||||3098|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3098A>C|||||3098|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1790A>C|||||1790|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1790A>C|||||1790|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*290A>C|||||290|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*290A>C|||||290|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:1964:1:15:0,-15.0567,-175.516

+NC_045512.2	10352	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1966;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10087A>C|p.Lys3363Gln|10087/21291|10087/21291|3363/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10087A>C|p.Lys3363Gln|10087/13218|10087/13218|3363/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.298A>C|p.Lys100Gln|298/918|298/918|100/305||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.298A>C|p.Lys100Gln|298/918|298/918|100/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-621A>C|||||621|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-621A>C|||||621|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1491A>C|||||1491|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1491A>C|||||1491|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1740A>C|||||1740|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1740A>C|||||1740|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2334A>C|||||2334|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2334A>C|||||2334|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2673A>C|||||2673|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2673A>C|||||2673|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3090A>C|||||3090|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3090A>C|||||3090|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1798A>C|||||1798|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1798A>C|||||1798|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*298A>C|||||298|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*298A>C|||||298|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:1966:1:9:0,-15.6567,-176.293

+NC_045512.2	10355	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=1;PAIREDR=0.759259;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1971;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10090T>C|p.Tyr3364His|10090/21291|10090/21291|3364/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10090T>C|p.Tyr3364His|10090/13218|10090/13218|3364/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.301T>C|p.Tyr101His|301/918|301/918|101/305||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.301T>C|p.Tyr101His|301/918|301/918|101/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-618T>C|||||618|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-618T>C|||||618|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1488T>C|||||1488|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1488T>C|||||1488|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1737T>C|||||1737|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1737T>C|||||1737|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2331T>C|||||2331|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2331T>C|||||2331|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2670T>C|||||2670|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2670T>C|||||2670|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3087T>C|||||3087|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3087T>C|||||3087|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1801T>C|||||1801|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1801T>C|||||1801|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*301T>C|||||301|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*301T>C|||||301|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:1971:1:9:0,-15.6567,-176.746

+NC_045512.2	10358	.	AA	TC	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=55;DPB=55;DPRA=0;EPP=5.18177;EPPR=3.6537;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=76.8511;PAIRED=0;PAIREDR=0.777778;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1937;RO=54;RPL=1;RPP=5.18177;RPPR=120.27;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.6537;SRR=25;TYPE=complex;ANN=TC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10093_10094delAAinsTC|p.Lys3365Ser|10093/21291|10093/21291|3365/7096||,TC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10093_10094delAAinsTC|p.Lys3365Ser|10093/13218|10093/13218|3365/4405||,TC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.304_305delAAinsTC|p.Lys102Ser|304/918|304/918|102/305||WARNING_TRANSCRIPT_NO_START_CODON,TC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.304_305delAAinsTC|p.Lys102Ser|304/918|304/918|102/305||WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-615_-614delAAinsTC|||||615|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-615_-614delAAinsTC|||||615|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1485_-1484delAAinsTC|||||1485|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1485_-1484delAAinsTC|||||1485|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1734_-1733delAAinsTC|||||1734|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1734_-1733delAAinsTC|||||1734|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2328_-2327delAAinsTC|||||2328|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2328_-2327delAAinsTC|||||2328|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2667_-2666delAAinsTC|||||2667|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2667_-2666delAAinsTC|||||2667|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3084_-3083delAAinsTC|||||3084|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3084_-3083delAAinsTC|||||3084|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1804_*1805delAAinsTC|||||1804|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1804_*1805delAAinsTC|||||1804|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*304_*305delAAinsTC|||||304|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*304_*305delAAinsTC|||||304|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:55:54,1:54:1937:1:9:0,-15.6567,-173.683

+NC_045512.2	10364	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.18177;EPPR=3.55317;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=84.7931;PAIRED=1;PAIREDR=0.796875;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=2326;RO=64;RPL=0;RPP=5.18177;RPPR=74.8046;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=39;SRP=9.66043;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10099G>T|p.Val3367Phe|10099/21291|10099/21291|3367/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10099G>T|p.Val3367Phe|10099/13218|10099/13218|3367/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.310G>T|p.Val104Phe|310/918|310/918|104/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.310G>T|p.Val104Phe|310/918|310/918|104/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-609G>T|||||609|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-609G>T|||||609|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1479G>T|||||1479|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1479G>T|||||1479|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1728G>T|||||1728|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1728G>T|||||1728|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2322G>T|||||2322|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2322G>T|||||2322|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2661G>T|||||2661|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2661G>T|||||2661|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3078G>T|||||3078|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3078G>T|||||3078|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1810G>T|||||1810|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1810G>T|||||1810|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*310G>T|||||310|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*310G>T|||||310|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:65:64,1:64:2326:1:34:0,-16.168,-206.182

+NC_045512.2	10377	.	C	A	7.68684E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=59;DPB=59;DPRA=0;EPP=5.18177;EPPR=15.1406;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=82.3261;PAIRED=1;PAIREDR=0.87931;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=2116;RO=58;RPL=1;RPP=5.18177;RPPR=41.348;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=5.40641;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10112C>A|p.Pro3371Gln|10112/21291|10112/21291|3371/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10112C>A|p.Pro3371Gln|10112/13218|10112/13218|3371/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.323C>A|p.Pro108Gln|323/918|323/918|108/305||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.323C>A|p.Pro108Gln|323/918|323/918|108/305||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-596C>A|||||596|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-596C>A|||||596|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1466C>A|||||1466|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1466C>A|||||1466|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1715C>A|||||1715|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1715C>A|||||1715|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2309C>A|||||2309|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2309C>A|||||2309|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2648C>A|||||2648|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2648C>A|||||2648|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3065C>A|||||3065|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3065C>A|||||3065|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1823C>A|||||1823|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1823C>A|||||1823|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*323C>A|||||323|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*323C>A|||||323|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:59:58,1:58:2116:1:9:0,-16.8608,-189.785

+NC_045512.2	10454	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.5895;PAIRED=1;PAIREDR=0.891892;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1359;RO=37;RPL=1;RPP=5.18177;RPPR=10.1116;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=14;SRP=7.76406;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10189T>G|p.Phe3397Val|10189/21291|10189/21291|3397/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10189T>G|p.Phe3397Val|10189/13218|10189/13218|3397/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.400T>G|p.Phe134Val|400/918|400/918|134/305||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.400T>G|p.Phe134Val|400/918|400/918|134/305||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-519T>G|||||519|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-519T>G|||||519|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1389T>G|||||1389|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1389T>G|||||1389|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1638T>G|||||1638|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1638T>G|||||1638|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2232T>G|||||2232|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2232T>G|||||2232|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2571T>G|||||2571|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2571T>G|||||2571|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2988T>G|||||2988|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2988T>G|||||2988|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1900T>G|||||1900|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1900T>G|||||1900|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*400T>G|||||400|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*400T>G|||||400|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1359:1:31:0,-8.33969,-119.502

+NC_045512.2	10548	.	T	G	2.08611E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6358;PAIRED=0;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1025;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10283T>G|p.Met3428Arg|10283/21291|10283/21291|3428/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10283T>G|p.Met3428Arg|10283/13218|10283/13218|3428/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.494T>G|p.Met165Arg|494/918|494/918|165/305||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.494T>G|p.Met165Arg|494/918|494/918|165/305||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-425T>G|||||425|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-425T>G|||||425|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1295T>G|||||1295|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1295T>G|||||1295|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1544T>G|||||1544|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1544T>G|||||1544|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2138T>G|||||2138|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2138T>G|||||2138|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2477T>G|||||2477|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2477T>G|||||2477|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2894T>G|||||2894|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2894T>G|||||2894|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1994T>G|||||1994|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1994T>G|||||1994|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*494T>G|||||494|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*494T>G|||||494|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:1025:1:11:0,-7.32884,-91.4635

+NC_045512.2	10602	.	G	T	2.08611E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.6358;PAIRED=0;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=989;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10337G>T|p.Gly3446Val|10337/21291|10337/21291|3446/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10337G>T|p.Gly3446Val|10337/13218|10337/13218|3446/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.548G>T|p.Gly183Val|548/918|548/918|183/305||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.548G>T|p.Gly183Val|548/918|548/918|183/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-371G>T|||||371|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-371G>T|||||371|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1241G>T|||||1241|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1241G>T|||||1241|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1490G>T|||||1490|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1490G>T|||||1490|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2084G>T|||||2084|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2084G>T|||||2084|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2423G>T|||||2423|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2423G>T|||||2423|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2840G>T|||||2840|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2840G>T|||||2840|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2048G>T|||||2048|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2048G>T|||||2048|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*548G>T|||||548|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*548G>T|||||548|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:989:1:11:0,-7.32884,-88.2152

+NC_045512.2	10649	.	A	C	2.08611E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=5.18177;EPPR=4.34659;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.2069;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=967;RO=26;RPL=1;RPP=5.18177;RPPR=59.4686;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=11;SRP=4.34659;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10384A>C|p.Thr3462Pro|10384/21291|10384/21291|3462/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10384A>C|p.Thr3462Pro|10384/13218|10384/13218|3462/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.595A>C|p.Thr199Pro|595/918|595/918|199/305||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.595A>C|p.Thr199Pro|595/918|595/918|199/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-324A>C|||||324|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-324A>C|||||324|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1194A>C|||||1194|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1194A>C|||||1194|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1443A>C|||||1443|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1443A>C|||||1443|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2037A>C|||||2037|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2037A>C|||||2037|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2376A>C|||||2376|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2376A>C|||||2376|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2793A>C|||||2793|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2793A>C|||||2793|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2095A>C|||||2095|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2095A>C|||||2095|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*595A>C|||||595|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*595A>C|||||595|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:27:26,1:26:967:1:7:0,-7.42781,-86.6456

+NC_045512.2	10672	.	T	G	1.34597E-8	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=17;DPB=17;DPRA=0;EPP=5.18177;EPPR=37.7539;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=19.5921;PAIRED=1;PAIREDR=0.875;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=606;RO=16;RPL=0;RPP=5.18177;RPPR=29.6108;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=1;SRP=29.6108;SRR=15;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10407T>G|p.Ala3469Ala|10407/21291|10407/21291|3469/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10407T>G|p.Ala3469Ala|10407/13218|10407/13218|3469/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.618T>G|p.Ala206Ala|618/918|618/918|206/305||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.618T>G|p.Ala206Ala|618/918|618/918|206/305||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-301T>G|||||301|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-301T>G|||||301|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1171T>G|||||1171|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1171T>G|||||1171|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1420T>G|||||1420|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1420T>G|||||1420|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2014T>G|||||2014|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2014T>G|||||2014|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2353T>G|||||2353|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2353T>G|||||2353|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2770T>G|||||2770|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2770T>G|||||2770|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2118T>G|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2118T>G|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*618T>G|||||618|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*618T>G|||||618|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:17:16,1:16:606:1:34:0,-1.7186,-51.4813

+NC_045512.2	10725	.	C	A	3.92939E-11	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.4284;PAIRED=0;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=722;RO=19;RPL=1;RPP=5.18177;RPPR=12.2676;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=12.2676;SRR=14;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10460C>A|p.Thr3487Asn|10460/21291|10460/21291|3487/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10460C>A|p.Thr3487Asn|10460/13218|10460/13218|3487/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.671C>A|p.Thr224Asn|671/918|671/918|224/305||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.671C>A|p.Thr224Asn|671/918|671/918|224/305||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-248C>A|||||248|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-248C>A|||||248|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1118C>A|||||1118|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1118C>A|||||1118|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1367C>A|||||1367|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1367C>A|||||1367|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1961C>A|||||1961|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1961C>A|||||1961|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2300C>A|||||2300|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2300C>A|||||2300|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2717C>A|||||2717|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2717C>A|||||2717|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2171C>A|||||2171|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2171C>A|||||2171|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*671C>A|||||671|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*671C>A|||||671|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:19,1:19:722:1:26:0,-3.42077,-62.7132

+NC_045512.2	10735	.	T	C	6.19167E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=22.6712;PAIRED=1;PAIREDR=0.894737;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=712;RO=19;RPL=1;RPP=5.18177;RPPR=12.2676;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=12.2676;SRR=14;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10470T>C|p.Leu3490Leu|10470/21291|10470/21291|3490/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10470T>C|p.Leu3490Leu|10470/13218|10470/13218|3490/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.681T>C|p.Leu227Leu|681/918|681/918|227/305||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.681T>C|p.Leu227Leu|681/918|681/918|227/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-238T>C|||||238|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-238T>C|||||238|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1108T>C|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1108T>C|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1357T>C|||||1357|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1357T>C|||||1357|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1951T>C|||||1951|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1951T>C|||||1951|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2290T>C|||||2290|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2290T>C|||||2290|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2707T>C|||||2707|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2707T>C|||||2707|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2181T>C|||||2181|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2181T>C|||||2181|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*681T>C|||||681|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*681T>C|||||681|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:19,1:19:712:1:38:0,-2.22333,-60.6137

+NC_045512.2	11001	.	C	A	4.479E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=5.18177;EPPR=50.7827;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.6076;PAIRED=1;PAIREDR=0.954545;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=768;RO=22;RPL=0;RPP=5.18177;RPPR=17.2236;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=17;SRP=17.2236;SRR=5;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10736C>A|p.Thr3579Lys|10736/21291|10736/21291|3579/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10736C>A|p.Thr3579Lys|10736/13218|10736/13218|3579/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.29C>A|p.Thr10Lys|29/870|29/870|10/289||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.29C>A|p.Thr10Lys|29/870|29/870|10/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-842C>A|||||842|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-842C>A|||||842|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1091C>A|||||1091|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1091C>A|||||1091|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1685C>A|||||1685|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1685C>A|||||1685|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2024C>A|||||2024|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2024C>A|||||2024|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2441C>A|||||2441|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2441C>A|||||2441|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2447C>A|||||2447|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2447C>A|||||2447|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*947C>A|||||947|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*947C>A|||||947|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*29C>A|||||29|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*29C>A|||||29|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:23:22,1:22:768:1:34:0,-3.52478,-66.0411

+NC_045512.2	11002	.	A	C	5.28118E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=7.35324;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.437;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=47;QR=791;RO=23;RPL=0;RPP=7.35324;RPPR=18.9659;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=18;SRP=18.9659;SRR=5;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10737A>C|p.Thr3579Thr|10737/21291|10737/21291|3579/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10737A>C|p.Thr3579Thr|10737/13218|10737/13218|3579/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.30A>C|p.Thr10Thr|30/870|30/870|10/289||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.30A>C|p.Thr10Thr|30/870|30/870|10/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-841A>C|||||841|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-841A>C|||||841|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1090A>C|||||1090|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1090A>C|||||1090|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1684A>C|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1684A>C|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2023A>C|||||2023|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2023A>C|||||2023|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2440A>C|||||2440|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2440A>C|||||2440|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2448A>C|||||2448|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2448A>C|||||2448|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*948A>C|||||948|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*948A>C|||||948|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*30A>C|||||30|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*30A>C|||||30|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:23,2:23:791:2:47:0,-3.06093,-67.0399

+NC_045512.2	11030	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3837;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1136;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10765A>T|p.Thr3589Ser|10765/21291|10765/21291|3589/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10765A>T|p.Thr3589Ser|10765/13218|10765/13218|3589/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.58A>T|p.Thr20Ser|58/870|58/870|20/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.58A>T|p.Thr20Ser|58/870|58/870|20/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-813A>T|||||813|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-813A>T|||||813|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1062A>T|||||1062|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1062A>T|||||1062|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1656A>T|||||1656|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1656A>T|||||1656|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1995A>T|||||1995|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1995A>T|||||1995|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2412A>T|||||2412|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2412A>T|||||2412|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2476A>T|||||2476|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2476A>T|||||2476|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*976A>T|||||976|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*976A>T|||||976|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*58A>T|||||58|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*58A>T|||||58|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1136:1:8:0,-8.53193,-101.747

+NC_045512.2	11035	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3837;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1137;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10770A>T|p.Ser3590Ser|10770/21291|10770/21291|3590/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10770A>T|p.Ser3590Ser|10770/13218|10770/13218|3590/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.63A>T|p.Ser21Ser|63/870|63/870|21/289||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.63A>T|p.Ser21Ser|63/870|63/870|21/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-808A>T|||||808|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-808A>T|||||808|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1057A>T|||||1057|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1057A>T|||||1057|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1651A>T|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1651A>T|||||1651|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1990A>T|||||1990|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1990A>T|||||1990|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2407A>T|||||2407|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2407A>T|||||2407|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2481A>T|||||2481|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2481A>T|||||2481|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*981A>T|||||981|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*981A>T|||||981|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*63A>T|||||63|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*63A>T|||||63|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1137:1:8:0,-8.53193,-101.836

+NC_045512.2	11038	.	T	A	2.14262E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=59.7581;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=37.9404;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=1136;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=24;SRP=26.4622;SRR=6;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10773T>A|p.Leu3591Leu|10773/21291|10773/21291|3591/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10773T>A|p.Leu3591Leu|10773/13218|10773/13218|3591/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.66T>A|p.Leu22Leu|66/870|66/870|22/289||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.66T>A|p.Leu22Leu|66/870|66/870|22/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-805T>A|||||805|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-805T>A|||||805|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1054T>A|||||1054|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1054T>A|||||1054|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1648T>A|||||1648|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1648T>A|||||1648|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1987T>A|||||1987|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1987T>A|||||1987|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2404T>A|||||2404|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2404T>A|||||2404|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2484T>A|||||2484|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2484T>A|||||2484|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*984T>A|||||984|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*984T>A|||||984|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*66T>A|||||66|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*66T>A|||||66|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1136:1:36:0,-5.73365,-98.9484

+NC_045512.2	11047	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=68.1545;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.3837;PAIRED=1;PAIREDR=0.966667;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1132;RO=30;RPL=0;RPP=5.18177;RPPR=31.9633;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=25;SRP=31.9633;SRR=5;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10782A>C|p.Leu3594Phe|10782/21291|10782/21291|3594/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10782A>C|p.Leu3594Phe|10782/13218|10782/13218|3594/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.75A>C|p.Leu25Phe|75/870|75/870|25/289||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.75A>C|p.Leu25Phe|75/870|75/870|25/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-796A>C|||||796|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-796A>C|||||796|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1045A>C|||||1045|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1045A>C|||||1045|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1639A>C|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1639A>C|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1978A>C|||||1978|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1978A>C|||||1978|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2395A>C|||||2395|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2395A>C|||||2395|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2493A>C|||||2493|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2493A>C|||||2493|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*993A>C|||||993|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*993A>C|||||993|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*75A>C|||||75|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*75A>C|||||75|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1132:1:8:0,-8.53193,-101.387

+NC_045512.2	11074	.	CTTTTTTTTGTATGA	CTTTTTTTGTATGA,CTTTTTTTTTTATGA	32.7069	.	AB=0.0344828,0.206897;ABP=57.5966,24.6501;AC=0,1;AF=0,0.5;AN=2;AO=1,6;CIGAR=1M1D13M,9M1X5M;DP=29;DPB=28.9333;DPRA=0,0;EPP=5.18177,8.80089;EPPR=34.9902;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=7.53051;PAIRED=1,1;PAIREDR=0.954545;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=38,227;QR=823;RO=22;RPL=0,0;RPP=5.18177,16.0391;RPPR=50.7827;RPR=1,6;RUN=1,1;SAF=1,5;SAP=5.18177,8.80089;SAR=0,1;SRF=20;SRP=34.9902;SRR=2;TYPE=del,snp;ANN=CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817delT|p.Leu3606fs|10817/21291|10817/21291|3606/7096||,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10817delT|p.Leu3606fs|10817/13218|10817/13218|3606/4405||,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.110delT|p.Leu37fs|110/870|110/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.110delT|p.Leu37fs|110/870|110/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10818G>T|p.Leu3606Phe|10818/21291|10818/21291|3606/7096||,CTTTTTTTTTTATGA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10818G>T|p.Leu3606Phe|10818/13218|10818/13218|3606/4405||,CTTTTTTTTTTATGA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.111G>T|p.Leu37Phe|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.111G>T|p.Leu37Phe|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-761delT|||||761|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-760G>T|||||760|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-761delT|||||761|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-760G>T|||||760|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1010delT|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1009G>T|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1010delT|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1009G>T|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1604delT|||||1604|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1603G>T|||||1603|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1604delT|||||1604|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1603G>T|||||1603|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1943delT|||||1943|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1942G>T|||||1942|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1943delT|||||1943|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1942G>T|||||1942|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2360delT|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2359G>T|||||2359|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2360delT|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2359G>T|||||2359|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2528delT|||||2528|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2529G>T|||||2529|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2528delT|||||2528|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2529G>T|||||2529|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1028delT|||||1028|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1029G>T|||||1029|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1028delT|||||1028|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1029G>T|||||1029|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*110delT|||||110|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*111G>T|||||111|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*110delT|||||110|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*111G>T|||||111|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/2:29:22,1,6:22:823:1,6:38,227:-11.9855,-15.4914,-82.5863,0,-64.2769,-65.5874

+NC_045512.2	11094	.	C	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=3.40914;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=70.2452;PAIRED=0;PAIREDR=0.959184;PAO=0;PQA=0;PQR=0;PRO=0;QA=8;QR=1679;RO=49;RPL=0;RPP=5.18177;RPPR=109.412;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.40914;SRR=23;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10829C>G|p.Ala3610Gly|10829/21291|10829/21291|3610/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10829C>G|p.Ala3610Gly|10829/13218|10829/13218|3610/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.122C>G|p.Ala41Gly|122/870|122/870|41/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.122C>G|p.Ala41Gly|122/870|122/870|41/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-749C>G|||||749|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-749C>G|||||749|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-998C>G|||||998|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-998C>G|||||998|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1592C>G|||||1592|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1592C>G|||||1592|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1931C>G|||||1931|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1931C>G|||||1931|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2348C>G|||||2348|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2348C>G|||||2348|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2540C>G|||||2540|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2540C>G|||||2540|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1040C>G|||||1040|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1040C>G|||||1040|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*122C>G|||||122|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*122C>G|||||122|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:50:49,1:49:1679:1:8:0,-14.2515,-150.57

+NC_045512.2	11127	.	T	G	1.11656E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.1156;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1951;RO=52;RPL=0;RPP=5.18177;RPPR=115.927;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10862T>G|p.Met3621Arg|10862/21291|10862/21291|3621/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10862T>G|p.Met3621Arg|10862/13218|10862/13218|3621/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.155T>G|p.Met52Arg|155/870|155/870|52/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.155T>G|p.Met52Arg|155/870|155/870|52/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-716T>G|||||716|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-716T>G|||||716|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-965T>G|||||965|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-965T>G|||||965|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1559T>G|||||1559|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1559T>G|||||1559|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1898T>G|||||1898|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1898T>G|||||1898|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2315T>G|||||2315|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2315T>G|||||2315|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2573T>G|||||2573|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2573T>G|||||2573|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1073T>G|||||1073|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1073T>G|||||1073|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*155T>G|||||155|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*155T>G|||||155|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1951:1:9:0,-15.0546,-174.948

+NC_045512.2	11148	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=7.18621;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.132;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=35;QR=1961;RO=52;RPL=0;RPP=5.18177;RPPR=83.8559;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10883T>C|p.Phe3628Ser|10883/21291|10883/21291|3628/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10883T>C|p.Phe3628Ser|10883/13218|10883/13218|3628/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.176T>C|p.Phe59Ser|176/870|176/870|59/289||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.176T>C|p.Phe59Ser|176/870|176/870|59/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-695T>C|||||695|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-695T>C|||||695|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-944T>C|||||944|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-944T>C|||||944|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1538T>C|||||1538|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1538T>C|||||1538|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1877T>C|||||1877|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1877T>C|||||1877|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2294T>C|||||2294|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2294T>C|||||2294|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2594T>C|||||2594|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2594T>C|||||2594|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1094T>C|||||1094|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1094T>C|||||1094|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*176T>C|||||176|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*176T>C|||||176|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1961:1:35:0,-12.456,-173.247

+NC_045512.2	11152	.	CAAACAT	CAACAT	3.57126E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D5M;DP=53;DPB=52.7143;DPRA=0;EPP=7.35324;EPPR=55.1682;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.8816;PAIRED=1;PAIREDR=0.921569;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1886;RO=51;RPL=1;RPP=3.0103;RPPR=15.3153;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.05288;SRR=26;TYPE=del;ANN=CAACAT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10890delA|p.Lys3630fs|10890/21291|10890/21291|3630/7096||,CAACAT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10890delA|p.Lys3630fs|10890/13218|10890/13218|3630/4405||,CAACAT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.183delA|p.Lys61fs|183/870|183/870|61/289||WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.183delA|p.Lys61fs|183/870|183/870|61/289||WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-688delA|||||688|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-688delA|||||688|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-937delA|||||937|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-937delA|||||937|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1531delA|||||1531|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1531delA|||||1531|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1870delA|||||1870|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1870delA|||||1870|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2287delA|||||2287|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2287delA|||||2287|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2601delA|||||2601|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2601delA|||||2601|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1101delA|||||1101|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1101delA|||||1101|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*183delA|||||183|WARNING_TRANSCRIPT_NO_START_CODON,CAACAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*183delA|||||183|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:51,2:51:1886:2:72:0,-9.11822,-163.168

+NC_045512.2	11208	.	C	A	1.36065E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=99.2232;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1950;RO=52;RPL=0;RPP=5.18177;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10943C>A|p.Ala3648Asp|10943/21291|10943/21291|3648/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10943C>A|p.Ala3648Asp|10943/13218|10943/13218|3648/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.236C>A|p.Ala79Asp|236/870|236/870|79/289||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.236C>A|p.Ala79Asp|236/870|236/870|79/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-635C>A|||||635|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-635C>A|||||635|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-884C>A|||||884|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-884C>A|||||884|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1478C>A|||||1478|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1478C>A|||||1478|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1817C>A|||||1817|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1817C>A|||||1817|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2234C>A|||||2234|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2234C>A|||||2234|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2654C>A|||||2654|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2654C>A|||||2654|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1154C>A|||||1154|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1154C>A|||||1154|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*236C>A|||||236|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*236C>A|||||236|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1950:1:11:0,-14.8546,-174.655

+NC_045512.2	11234	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=63.3104;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=68.3616;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1919;RO=52;RPL=0;RPP=5.18177;RPPR=11.1951;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10969G>A|p.Ala3657Thr|10969/21291|10969/21291|3657/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10969G>A|p.Ala3657Thr|10969/13218|10969/13218|3657/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.262G>A|p.Ala88Thr|262/870|262/870|88/289||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.262G>A|p.Ala88Thr|262/870|262/870|88/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-609G>A|||||609|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-609G>A|||||609|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-858G>A|||||858|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-858G>A|||||858|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1452G>A|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1452G>A|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1791G>A|||||1791|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1791G>A|||||1791|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2208G>A|||||2208|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2208G>A|||||2208|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2680G>A|||||2680|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2680G>A|||||2680|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1180G>A|||||1180|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1180G>A|||||1180|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*262G>A|||||262|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*262G>A|||||262|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1919:1:34:0,-12.5557,-169.565

+NC_045512.2	11242	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=5.68288;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1915;RO=52;RPL=1;RPP=5.18177;RPPR=83.8559;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=3.0103;SRR=26;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10977G>T|p.Trp3659Cys|10977/21291|10977/21291|3659/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10977G>T|p.Trp3659Cys|10977/13218|10977/13218|3659/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.270G>T|p.Trp90Cys|270/870|270/870|90/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.270G>T|p.Trp90Cys|270/870|270/870|90/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-601G>T|||||601|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-601G>T|||||601|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-850G>T|||||850|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-850G>T|||||850|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1444G>T|||||1444|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1444G>T|||||1444|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1783G>T|||||1783|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1783G>T|||||1783|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2200G>T|||||2200|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2200G>T|||||2200|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4995G>T|||||4995|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2688G>T|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2688G>T|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1188G>T|||||1188|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1188G>T|||||1188|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*270G>T|||||270|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*270G>T|||||270|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1915:1:11:0,-14.8546,-171.508

+NC_045512.2	11261	.	T	G	1.36065E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1870;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10996T>G|p.Trp3666Gly|10996/21291|10996/21291|3666/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10996T>G|p.Trp3666Gly|10996/13218|10996/13218|3666/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.289T>G|p.Trp97Gly|289/870|289/870|97/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.289T>G|p.Trp97Gly|289/870|289/870|97/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-582T>G|||||582|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-582T>G|||||582|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-831T>G|||||831|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-831T>G|||||831|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1425T>G|||||1425|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1425T>G|||||1425|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1764T>G|||||1764|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1764T>G|||||1764|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2181T>G|||||2181|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2181T>G|||||2181|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4976T>G|||||4976|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2707T>G|||||2707|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2707T>G|||||2707|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1207T>G|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1207T>G|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*289T>G|||||289|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*289T>G|||||289|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1870:1:11:0,-14.8546,-167.457

+NC_045512.2	11262	.	G	A	5.89167E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.7413;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=28;QR=1853;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10997G>A|p.Trp3666*|10997/21291|10997/21291|3666/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10997G>A|p.Trp3666*|10997/13218|10997/13218|3666/4405||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.290G>A|p.Trp97*|290/870|290/870|97/289||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.290G>A|p.Trp97*|290/870|290/870|97/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-581G>A|||||581|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-581G>A|||||581|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-830G>A|||||830|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-830G>A|||||830|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1424G>A|||||1424|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1424G>A|||||1424|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1763G>A|||||1763|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1763G>A|||||1763|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2180G>A|||||2180|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2180G>A|||||2180|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4975G>A|||||4975|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2708G>A|||||2708|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2708G>A|||||2708|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1208G>A|||||1208|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1208G>A|||||1208|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*290G>A|||||290|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*290G>A|||||290|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1853:1:28:0,-13.1549,-164.222

+NC_045512.2	11269	.	TA	GT	1.36065E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=2X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=2;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.6551;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1870;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11004_11005delTAinsGT|p.AspMet3668GluLeu|11004/21291|11004/21291|3668/7096||,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11004_11005delTAinsGT|p.AspMet3668GluLeu|11004/13218|11004/13218|3668/4405||,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.297_298delTAinsGT|p.AspMet99GluLeu|297/870|297/870|99/289||WARNING_TRANSCRIPT_NO_START_CODON,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.297_298delTAinsGT|p.AspMet99GluLeu|297/870|297/870|99/289||WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-574_-573delTAinsGT|||||574|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-574_-573delTAinsGT|||||574|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-823_-822delTAinsGT|||||823|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-823_-822delTAinsGT|||||823|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1417_-1416delTAinsGT|||||1417|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1417_-1416delTAinsGT|||||1417|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1756_-1755delTAinsGT|||||1756|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1756_-1755delTAinsGT|||||1756|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2173_-2172delTAinsGT|||||2173|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2173_-2172delTAinsGT|||||2173|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4968_-4967delTAinsGT|||||4968|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2715_*2716delTAinsGT|||||2715|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2715_*2716delTAinsGT|||||2715|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1215_*1216delTAinsGT|||||1215|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1215_*1216delTAinsGT|||||1215|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*297_*298delTAinsGT|||||297|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*297_*298delTAinsGT|||||297|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1870:1:11:0,-14.8546,-167.46

+NC_045512.2	11271	.	TGGT	CGGG	1.39076E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X2M1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.1946;PAIRED=0;PAIREDR=0.942308;PAO=0;PQA=0;PQR=0;PRO=0;QA=13;QR=1883;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=complex;ANN=CGGG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11006_11009delTGGTinsCGGG|p.MetVal3669ThrGly|11006/21291|11006/21291|3669/7096||,CGGG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11006_11009delTGGTinsCGGG|p.MetVal3669ThrGly|11006/13218|11006/13218|3669/4405||,CGGG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.299_302delTGGTinsCGGG|p.MetVal100ThrGly|299/870|299/870|100/289||WARNING_TRANSCRIPT_NO_START_CODON,CGGG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.299_302delTGGTinsCGGG|p.MetVal100ThrGly|299/870|299/870|100/289||WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-572_-569delTGGTinsCGGG|||||572|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-572_-569delTGGTinsCGGG|||||572|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-821_-818delTGGTinsCGGG|||||821|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-821_-818delTGGTinsCGGG|||||821|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1415_-1412delTGGTinsCGGG|||||1415|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1415_-1412delTGGTinsCGGG|||||1415|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1754_-1751delTGGTinsCGGG|||||1754|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1754_-1751delTGGTinsCGGG|||||1754|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2171_-2168delTGGTinsCGGG|||||2171|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2171_-2168delTGGTinsCGGG|||||2171|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4966_-4963delTGGTinsCGGG|||||4966|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2717_*2720delTGGTinsCGGG|||||2717|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2717_*2720delTGGTinsCGGG|||||2717|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1217_*1220delTGGTinsCGGG|||||1217|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1217_*1220delTGGTinsCGGG|||||1217|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*299_*302delTGGTinsCGGG|||||299|WARNING_TRANSCRIPT_NO_START_CODON,CGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*299_*302delTGGTinsCGGG|||||299|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1883:1:13:0,-14.6546,-168.432

+NC_045512.2	11276	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.5761;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=7;QR=1851;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11011G>T|p.Asp3671Tyr|11011/21291|11011/21291|3671/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11011G>T|p.Asp3671Tyr|11011/13218|11011/13218|3671/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.304G>T|p.Asp102Tyr|304/870|304/870|102/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.304G>T|p.Asp102Tyr|304/870|304/870|102/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-567G>T|||||567|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-567G>T|||||567|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-816G>T|||||816|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-816G>T|||||816|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1410G>T|||||1410|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1410G>T|||||1410|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1749G>T|||||1749|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1749G>T|||||1749|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2166G>T|||||2166|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2166G>T|||||2166|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4961G>T|||||4961|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2722G>T|||||2722|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2722G>T|||||2722|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1222G>T|||||1222|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1222G>T|||||1222|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*304G>T|||||304|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*304G>T|||||304|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1851:1:7:0,-15.2546,-166.142

+NC_045512.2	11277	.	ATAC	TTCT	1.11656E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X1M2X;DP=53;DPB=53;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=4;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=74.1156;PAIRED=1;PAIREDR=0.923077;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1816;RO=52;RPL=1;RPP=5.18177;RPPR=115.927;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.17734;SRR=27;TYPE=complex;ANN=TTCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11012_11015delATACinsTTCT|p.AspThr3671ValLeu|11012/21291|11012/21291|3671/7096||,TTCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11012_11015delATACinsTTCT|p.AspThr3671ValLeu|11012/13218|11012/13218|3671/4405||,TTCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.305_308delATACinsTTCT|p.AspThr102ValLeu|305/870|305/870|102/289||WARNING_TRANSCRIPT_NO_START_CODON,TTCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.305_308delATACinsTTCT|p.AspThr102ValLeu|305/870|305/870|102/289||WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-566_-563delATACinsTTCT|||||566|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-566_-563delATACinsTTCT|||||566|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-815_-812delATACinsTTCT|||||815|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-815_-812delATACinsTTCT|||||815|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1409_-1406delATACinsTTCT|||||1409|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1409_-1406delATACinsTTCT|||||1409|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1748_-1745delATACinsTTCT|||||1748|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1748_-1745delATACinsTTCT|||||1748|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2165_-2162delATACinsTTCT|||||2165|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2165_-2162delATACinsTTCT|||||2165|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4960_-4957delATACinsTTCT|||||4960|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2723_*2726delATACinsTTCT|||||2723|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2723_*2726delATACinsTTCT|||||2723|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1223_*1226delATACinsTTCT|||||1223|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1223_*1226delATACinsTTCT|||||1223|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*305_*308delATACinsTTCT|||||305|WARNING_TRANSCRIPT_NO_START_CODON,TTCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*305_*308delATACinsTTCT|||||305|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:53:52,1:52:1816:1:9:0,-15.0546,-162.795

+NC_045512.2	11287	.	GTCTGGTTTTAAG	GAAG,GTCTGGTTTTTAAG	655.65	.	AB=0.681818,0.181818;ABP=15.6443,41.702;AC=1,1;AF=0.5,0.5;AN=2;AO=30,8;CIGAR=1M9D3M,6M1I7M;DP=44;DPB=23.8462;DPRA=0,0;EPP=4.16842,7.35324;EPPR=4.45795;GTI=0;LEN=9,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=12.3816;PAIRED=0.933333,0.875;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=977,299;QR=220;RO=6;RPL=30,8;RPP=68.1545,20.3821;RPPR=16.0391;RPR=0,0;RUN=1,1;SAF=13,2;SAP=4.16842,7.35324;SAR=17,6;SRF=2;SRP=4.45795;SRR=4;TYPE=del,ins;ANN=GTCTGGTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11031dupT|p.Lys3678fs|11032/21291|11032/21291|3678/7096||,GTCTGGTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11031dupT|p.Lys3678fs|11032/13218|11032/13218|3678/4405||,GTCTGGTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.324dupT|p.Lys109fs|325/870|325/870|109/289||WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.324dupT|p.Lys109fs|325/870|325/870|109/289||WARNING_TRANSCRIPT_NO_START_CODON,GAAG|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11023_11031delTCTGGTTTT|p.Ser3675_Phe3677del|11023/21291|11023/21291|3675/7096||,GAAG|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11023_11031delTCTGGTTTT|p.Ser3675_Phe3677del|11023/13218|11023/13218|3675/4405||,GAAG|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.316_324delTCTGGTTTT|p.Ser106_Phe108del|316/870|316/870|106/289||WARNING_TRANSCRIPT_NO_START_CODON,GAAG|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.316_324delTCTGGTTTT|p.Ser106_Phe108del|316/870|316/870|106/289||WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-555_-547delTCTGGTTTT|||||555|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-547dupT|||||546|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-555_-547delTCTGGTTTT|||||555|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-547dupT|||||546|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-804_-796delTCTGGTTTT|||||804|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-796dupT|||||795|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-804_-796delTCTGGTTTT|||||804|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-796dupT|||||795|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1398_-1390delTCTGGTTTT|||||1398|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1390dupT|||||1389|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1398_-1390delTCTGGTTTT|||||1398|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1390dupT|||||1389|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1737_-1729delTCTGGTTTT|||||1737|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1729dupT|||||1728|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1737_-1729delTCTGGTTTT|||||1737|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1729dupT|||||1728|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2154_-2146delTCTGGTTTT|||||2154|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2146dupT|||||2145|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2154_-2146delTCTGGTTTT|||||2154|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2146dupT|||||2145|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4949_-4941delTCTGGTTTT|||||4949|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4941dupT|||||4940|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2734_*2742delTCTGGTTTT|||||2734|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2742dupT|||||2743|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2734_*2742delTCTGGTTTT|||||2734|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2742dupT|||||2743|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1234_*1242delTCTGGTTTT|||||1234|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1242dupT|||||1243|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1234_*1242delTCTGGTTTT|||||1234|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1242dupT|||||1243|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*316_*324delTCTGGTTTT|||||316|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*324dupT|||||325|WARNING_TRANSCRIPT_NO_START_CODON,GAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*316_*324delTCTGGTTTT|||||316|WARNING_TRANSCRIPT_NO_START_CODON,GTCTGGTTTTTAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*324dupT|||||325|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	1/2:44:6,30,8:6:220:30,8:977,299:-83.515,-6.50958,-15.4575,-60.8267,0,-76.4071

+NC_045512.2	11308	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=57;DPB=57;DPRA=0;EPP=5.18177;EPPR=29.2231;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=73.8341;PAIRED=1;PAIREDR=0.946429;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1967;RO=56;RPL=0;RPP=5.18177;RPPR=33.4109;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=29;SRP=3.16541;SRR=27;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11043C>A|p.Asp3681Glu|11043/21291|11043/21291|3681/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11043C>A|p.Asp3681Glu|11043/13218|11043/13218|3681/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.336C>A|p.Asp112Glu|336/870|336/870|112/289||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.336C>A|p.Asp112Glu|336/870|336/870|112/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-535C>A|||||535|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-535C>A|||||535|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-784C>A|||||784|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-784C>A|||||784|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1378C>A|||||1378|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1378C>A|||||1378|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1717C>A|||||1717|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1717C>A|||||1717|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2134C>A|||||2134|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2134C>A|||||2134|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4929C>A|||||4929|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2754C>A|||||2754|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2754C>A|||||2754|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1254C>A|||||1254|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1254C>A|||||1254|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*336C>A|||||336|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*336C>A|||||336|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:57:56,1:56:1967:1:34:0,-13.7598,-173.887

+NC_045512.2	11324	.	T	C	9.58348E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=88.4369;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=60.612;PAIRED=1;PAIREDR=0.93617;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1724;RO=47;RPL=0;RPP=5.18177;RPPR=8.60069;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=5.27418;SRR=27;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11059T>C|p.Ser3687Pro|11059/21291|11059/21291|3687/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11059T>C|p.Ser3687Pro|11059/13218|11059/13218|3687/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.352T>C|p.Ser118Pro|352/870|352/870|118/289||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.352T>C|p.Ser118Pro|352/870|352/870|118/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-519T>C|||||519|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-519T>C|||||519|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-768T>C|||||768|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-768T>C|||||768|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1362T>C|||||1362|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1362T>C|||||1362|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1701T>C|||||1701|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1701T>C|||||1701|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2118T>C|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2118T>C|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4913T>C|||||4913|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2770T>C|||||2770|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2770T>C|||||2770|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1270T>C|||||1270|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1270T>C|||||1270|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*352T>C|||||352|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*352T>C|||||352|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:47,1:47:1724:1:38:0,-10.6522,-151.622

+NC_045512.2	11369	.	G	T	6.14782E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2468;PAIRED=1;PAIREDR=0.934783;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1747;RO=46;RPL=1;RPP=5.18177;RPPR=3.76559;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.76559;SRR=25;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11104G>T|p.Asp3702Tyr|11104/21291|11104/21291|3702/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11104G>T|p.Asp3702Tyr|11104/13218|11104/13218|3702/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.397G>T|p.Asp133Tyr|397/870|397/870|133/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.397G>T|p.Asp133Tyr|397/870|397/870|133/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-474G>T|||||474|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-474G>T|||||474|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-723G>T|||||723|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-723G>T|||||723|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1317G>T|||||1317|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1317G>T|||||1317|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1656G>T|||||1656|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1656G>T|||||1656|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2073G>T|||||2073|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2073G>T|||||2073|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4868G>T|||||4868|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2815G>T|||||2815|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2815G>T|||||2815|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1315G>T|||||1315|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1315G>T|||||1315|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*397G>T|||||397|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*397G>T|||||397|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:47:46,1:46:1747:1:38:0,-10.3511,-153.7

+NC_045512.2	11377	.	T	G	1.36214E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.1244;PAIRED=1;PAIREDR=0.931818;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1650;RO=44;RPL=1;RPP=5.18177;RPPR=3.20771;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.20771;SRR=23;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11112T>G|p.Gly3704Gly|11112/21291|11112/21291|3704/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11112T>G|p.Gly3704Gly|11112/13218|11112/13218|3704/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.405T>G|p.Gly135Gly|405/870|405/870|135/289||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.405T>G|p.Gly135Gly|405/870|405/870|135/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-466T>G|||||466|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-466T>G|||||466|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-715T>G|||||715|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-715T>G|||||715|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1309T>G|||||1309|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1309T>G|||||1309|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1648T>G|||||1648|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1648T>G|||||1648|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2065T>G|||||2065|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2065T>G|||||2065|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4860T>G|||||4860|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2823T>G|||||2823|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2823T>G|||||2823|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1323T>G|||||1323|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1323T>G|||||1323|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*405T>G|||||405|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*405T>G|||||405|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1650:1:31:0,-10.4469,-145.676

+NC_045512.2	11437	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=3.22745;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.5065;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1504;RO=40;RPL=0;RPP=5.18177;RPPR=89.8692;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11172T>G|p.Gly3724Gly|11172/21291|11172/21291|3724/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11172T>G|p.Gly3724Gly|11172/13218|11172/13218|3724/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.465T>G|p.Gly155Gly|465/870|465/870|155/289||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.465T>G|p.Gly155Gly|465/870|465/870|155/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-406T>G|||||406|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-406T>G|||||406|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-655T>G|||||655|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-655T>G|||||655|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1249T>G|||||1249|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1249T>G|||||1249|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1588T>G|||||1588|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1588T>G|||||1588|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2005T>G|||||2005|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2005T>G|||||2005|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4800T>G|||||4800|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2883T>G|||||2883|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2883T>G|||||2883|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1383T>G|||||1383|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1383T>G|||||1383|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*465T>G|||||465|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*465T>G|||||465|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1504:1:10:0,-11.3422,-134.644

+NC_045512.2	11515	.	T	G	3.51075E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.2763;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=1511;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=3.22745;SRR=19;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11250T>G|p.Thr3750Thr|11250/21291|11250/21291|3750/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11250T>G|p.Thr3750Thr|11250/13218|11250/13218|3750/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.543T>G|p.Thr181Thr|543/870|543/870|181/289||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.543T>G|p.Thr181Thr|543/870|543/870|181/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-328T>G|||||328|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-328T>G|||||328|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-577T>G|||||577|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-577T>G|||||577|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1171T>G|||||1171|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1171T>G|||||1171|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1510T>G|||||1510|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1510T>G|||||1510|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1927T>G|||||1927|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1927T>G|||||1927|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4722T>G|||||4722|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2961T>G|||||2961|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2961T>G|||||2961|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1461T>G|||||1461|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1461T>G|||||1461|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*543T>G|||||543|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*543T>G|||||543|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1511:1:11:0,-11.2422,-135.173

+NC_045512.2	11516	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=7.35324;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.8938;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1423;RO=39;RPL=1;RPP=3.0103;RPPR=3.06598;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11251G>A|p.Val3751Ile|11251/21291|11251/21291|3751/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11251G>A|p.Val3751Ile|11251/13218|11251/13218|3751/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.544G>A|p.Val182Ile|544/870|544/870|182/289||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.544G>A|p.Val182Ile|544/870|544/870|182/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-327G>A|||||327|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-327G>A|||||327|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-576G>A|||||576|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-576G>A|||||576|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1170G>A|||||1170|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1170G>A|||||1170|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1509G>A|||||1509|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1509G>A|||||1509|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1926G>A|||||1926|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1926G>A|||||1926|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4721G>A|||||4721|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2962G>A|||||2962|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2962G>A|||||2962|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1462G>A|||||1462|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1462G>A|||||1462|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*544G>A|||||544|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*544G>A|||||544|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:39,2:39:1423:2:76:0,-5.12742,-121.131

+NC_045512.2	11586	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=18.709;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=86.2051;PAIRED=1;PAIREDR=0.934426;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=2258;RO=61;RPL=1;RPP=5.18177;RPPR=15.8611;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=18.709;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11321A>T|p.Asn3774Ile|11321/21291|11321/21291|3774/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11321A>T|p.Asn3774Ile|11321/13218|11321/13218|3774/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.614A>T|p.Asn205Ile|614/870|614/870|205/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.614A>T|p.Asn205Ile|614/870|614/870|205/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-257A>T|||||257|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-257A>T|||||257|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-506A>T|||||506|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-506A>T|||||506|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1100A>T|||||1100|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1100A>T|||||1100|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1439A>T|||||1439|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1439A>T|||||1439|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1856A>T|||||1856|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1856A>T|||||1856|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4651A>T|||||4651|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3032A>T|||||3032|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3032A>T|||||3032|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1532A>T|||||1532|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1532A>T|||||1532|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*614A>T|||||614|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*614A>T|||||614|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2258:1:10:0,-17.6639,-202.456

+NC_045512.2	11589	.	C	T	3.76714E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=15.8611;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.2224;PAIRED=0;PAIREDR=0.95082;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=2222;RO=61;RPL=0;RPP=5.18177;RPPR=18.709;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=41;SRP=18.709;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11324C>T|p.Thr3775Ile|11324/21291|11324/21291|3775/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11324C>T|p.Thr3775Ile|11324/13218|11324/13218|3775/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.617C>T|p.Thr206Ile|617/870|617/870|206/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.617C>T|p.Thr206Ile|617/870|617/870|206/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-254C>T|||||254|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-254C>T|||||254|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-503C>T|||||503|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-503C>T|||||503|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1097C>T|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1097C>T|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1436C>T|||||1436|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1436C>T|||||1436|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1853C>T|||||1853|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1853C>T|||||1853|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4648C>T|||||4648|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3035C>T|||||3035|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3035C>T|||||3035|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1535C>T|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1535C>T|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*617C>T|||||617|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*617C>T|||||617|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2222:1:36:0,-15.0656,-196.615

+NC_045512.2	11803	.	T	C	9.08766E-17	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=43.538;PAIRED=1;PAIREDR=0.925;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=1458;RO=40;RPL=2;RPP=7.35324;RPPR=89.8692;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11538T>C|p.Gly3846Gly|11538/21291|11538/21291|3846/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11538T>C|p.Gly3846Gly|11538/13218|11538/13218|3846/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.831T>C|p.Gly277Gly|831/870|831/870|277/289||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.831T>C|p.Gly277Gly|831/870|831/870|277/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-40T>C|||||40|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-40T>C|||||40|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-289T>C|||||289|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-289T>C|||||289|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-883T>C|||||883|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-883T>C|||||883|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1222T>C|||||1222|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1222T>C|||||1222|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1639T>C|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1639T>C|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4434T>C|||||4434|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3249T>C|||||3249|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3249T>C|||||3249|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1749T>C|||||1749|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1749T>C|||||1749|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*831T>C|||||831|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*831T>C|||||831|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:40,2:40:1458:2:70:0,-5.99593,-124.851

+NC_045512.2	11808	.	GTGGC	TTGGT	9.40266E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X3M1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=5;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.4872;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=16;QR=1496;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=complex;ANN=TTGGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11543_11547delGTGGCinsTTGGT|p.Gly3848Val|11543/21291|11543/21291|3848/7096||,TTGGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11543_11547delGTGGCinsTTGGT|p.Gly3848Val|11543/13218|11543/13218|3848/4405||,TTGGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.836_840delGTGGCinsTTGGT|p.Gly279Val|836/870|836/870|279/289||WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.836_840delGTGGCinsTTGGT|p.Gly279Val|836/870|836/870|279/289||WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-35_-31delGTGGCinsTTGGT|||||35|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-35_-31delGTGGCinsTTGGT|||||35|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-284_-280delGTGGCinsTTGGT|||||284|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-284_-280delGTGGCinsTTGGT|||||284|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-878_-874delGTGGCinsTTGGT|||||878|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-878_-874delGTGGCinsTTGGT|||||878|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1217_-1213delGTGGCinsTTGGT|||||1217|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1217_-1213delGTGGCinsTTGGT|||||1217|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1634_-1630delGTGGCinsTTGGT|||||1634|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1634_-1630delGTGGCinsTTGGT|||||1634|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4429_-4425delGTGGCinsTTGGT|||||4429|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3254_*3258delGTGGCinsTTGGT|||||3254|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3254_*3258delGTGGCinsTTGGT|||||3254|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1754_*1758delGTGGCinsTTGGT|||||1754|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1754_*1758delGTGGCinsTTGGT|||||1754|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*836_*840delGTGGCinsTTGGT|||||836|WARNING_TRANSCRIPT_NO_START_CODON,TTGGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*836_*840delGTGGCinsTTGGT|||||836|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1496:1:16:0,-11.0433,-133.323

+NC_045512.2	11824	.	C	A	1.79352E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.8687;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1525;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11559C>A|p.Ile3853Ile|11559/21291|11559/21291|3853/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11559C>A|p.Ile3853Ile|11559/13218|11559/13218|3853/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.852C>A|p.Ile284Ile|852/870|852/870|284/289||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.852C>A|p.Ile284Ile|852/870|852/870|284/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-19C>A|||||19|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-19C>A|||||19|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-268C>A|||||268|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-268C>A|||||268|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-862C>A|||||862|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-862C>A|||||862|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1201C>A|||||1201|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1201C>A|||||1201|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1618C>A|||||1618|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1618C>A|||||1618|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4413C>A|||||4413|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3270C>A|||||3270|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3270C>A|||||3270|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1770C>A|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1770C>A|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*852C>A|||||852|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*852C>A|||||852|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1525:1:10:0,-11.6433,-136.532

+NC_045512.2	11828	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.257;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=1546;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11563G>T|p.Val3855Leu|11563/21291|11563/21291|3855/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11563G>T|p.Val3855Leu|11563/13218|11563/13218|3855/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.856G>T|p.Val286Leu|856/870|856/870|286/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.856G>T|p.Val286Leu|856/870|856/870|286/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-15G>T|||||15|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-15G>T|||||15|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-264G>T|||||264|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-264G>T|||||264|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-858G>T|||||858|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-858G>T|||||858|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1197G>T|||||1197|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1197G>T|||||1197|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1614G>T|||||1614|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1614G>T|||||1614|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4409G>T|||||4409|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3274G>T|||||3274|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3274G>T|||||3274|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1774G>T|||||1774|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1774G>T|||||1774|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*856G>T|||||856|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*856G>T|||||856|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1546:1:17:0,-10.9433,-137.722

+NC_045512.2	11833	.	C	T	4.46001E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1449;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11568C>T|p.Ala3856Ala|11568/21291|11568/21291|3856/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11568C>T|p.Ala3856Ala|11568/13218|11568/13218|3856/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.861C>T|p.Ala287Ala|861/870|861/870|287/289||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.861C>T|p.Ala287Ala|861/870|861/870|287/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-10C>T|||||10|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-10C>T|||||10|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-259C>T|||||259|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-259C>T|||||259|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-853C>T|||||853|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-853C>T|||||853|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1192C>T|||||1192|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1192C>T|||||1192|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1609C>T|||||1609|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1609C>T|||||1609|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4404C>T|||||4404|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3279C>T|||||3279|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3279C>T|||||3279|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1779C>T|||||1779|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1779C>T|||||1779|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*861C>T|||||861|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*861C>T|||||861|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1449:1:9:0,-11.7433,-129.785

+NC_045512.2	11840	.	C	T	4.46001E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=42;DPB=42;DPRA=0;EPP=5.18177;EPPR=3.06326;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.099;PAIRED=0;PAIREDR=0.95122;PAO=0;PQA=0;PQR=0;PRO=0;QA=9;QR=1510;RO=41;RPL=1;RPP=5.18177;RPPR=92.0407;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.06326;SRR=21;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11575C>T|p.Gln3859*|11575/21291|11575/21291|3859/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11575C>T|p.Gln3859*|11575/13218|11575/13218|3859/4405||,T|stop_gained&splice_region_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.868C>T|p.Gln290*|868/870|868/870|290/289||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained&splice_region_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.868C>T|p.Gln290*|868/870|868/870|290/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3C>T|||||3|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3C>T|||||3|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-252C>T|||||252|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-252C>T|||||252|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-846C>T|||||846|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-846C>T|||||846|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1185C>T|||||1185|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1185C>T|||||1185|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1602C>T|||||1602|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1602C>T|||||1602|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4397C>T|||||4397|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3286C>T|||||3286|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3286C>T|||||3286|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1786C>T|||||1786|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1786C>T|||||1786|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*868C>T|||||868|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*868C>T|||||868|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:42:41,1:41:1510:1:9:0,-11.7433,-135.281

+NC_045512.2	11854	.	A	G	1.67144E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=26;DPB=26;DPRA=0;EPP=3.0103;EPPR=26.1727;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=21.6781;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=908;RO=24;RPL=2;RPP=7.35324;RPPR=55.1256;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=26.1727;SRR=20;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11589A>G|p.Ser3863Ser|11589/21291|11589/21291|3863/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11589A>G|p.Ser3863Ser|11589/13218|11589/13218|3863/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.12A>G|p.Ser4Ser|12/249|12/249|4/82||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.12A>G|p.Ser4Ser|12/249|12/249|4/82||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-238A>G|||||238|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-238A>G|||||238|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-832A>G|||||832|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-832A>G|||||832|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1171A>G|||||1171|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1171A>G|||||1171|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1588A>G|||||1588|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1588A>G|||||1588|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4383A>G|||||4383|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3300A>G|||||3300|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3300A>G|||||3300|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1800A>G|||||1800|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1800A>G|||||1800|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*882A>G|||||882|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*882A>G|||||882|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*12A>G|||||12|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*12A>G|||||12|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:26:24,2:24:908:2:73:0,-0.895676,-75.11

+NC_045512.2	11880	.	TAC	TC	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=41;DPB=40.6667;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.0656;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1520;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.22745;SRR=21;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11616delA|p.Leu3872fs|11616/21291|11616/21291|3872/7096||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11616delA|p.Leu3872fs|11616/13218|11616/13218|3872/4405||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.39delA|p.Leu13fs|39/249|39/249|13/82||WARNING_TRANSCRIPT_NO_START_CODON,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.39delA|p.Leu13fs|39/249|39/249|13/82||WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-211delA|||||211|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-211delA|||||211|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-805delA|||||805|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-805delA|||||805|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1144delA|||||1144|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1144delA|||||1144|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1561delA|||||1561|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1561delA|||||1561|WARNING_TRANSCRIPT_NO_START_CODON,TC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4356delA|||||4356|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3327delA|||||3327|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3327delA|||||3327|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1827delA|||||1827|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1827delA|||||1827|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*909delA|||||909|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*909delA|||||909|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*39delA|||||39|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*39delA|||||39|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1520:1:38:0,-8.54496,-133.284

+NC_045512.2	11886	.	C	T	48.6984	.	AB=0.219512;ABP=31.0276;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=22.5536;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.2132;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=1216;RO=32;RPL=9;RPP=22.5536;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=20;SRP=7.35324;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11621C>T|p.Ser3874Leu|11621/21291|11621/21291|3874/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11621C>T|p.Ser3874Leu|11621/13218|11621/13218|3874/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.44C>T|p.Ser15Leu|44/249|44/249|15/82||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.44C>T|p.Ser15Leu|44/249|44/249|15/82||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-206C>T|||||206|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-206C>T|||||206|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-800C>T|||||800|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-800C>T|||||800|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1139C>T|||||1139|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1139C>T|||||1139|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1556C>T|||||1556|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1556C>T|||||1556|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4351C>T|||||4351|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3332C>T|||||3332|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3332C>T|||||3332|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1832C>T|||||1832|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1832C>T|||||1832|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*914C>T|||||914|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*914C>T|||||914|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*44C>T|||||44|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*44C>T|||||44|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:32,9:32:1216:9:342:-18.7954,0,-97.3988

+NC_045512.2	11896	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.0656;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1520;RO=40;RPL=0;RPP=5.18177;RPPR=3.22745;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=19;SRP=3.22745;SRR=21;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11631A>G|p.Gln3877Gln|11631/21291|11631/21291|3877/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11631A>G|p.Gln3877Gln|11631/13218|11631/13218|3877/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.54A>G|p.Gln18Gln|54/249|54/249|18/82||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.54A>G|p.Gln18Gln|54/249|54/249|18/82||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-196A>G|||||196|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-196A>G|||||196|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-790A>G|||||790|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-790A>G|||||790|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1129A>G|||||1129|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1129A>G|||||1129|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1546A>G|||||1546|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1546A>G|||||1546|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4341A>G|||||4341|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3342A>G|||||3342|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3342A>G|||||3342|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1842A>G|||||1842|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1842A>G|||||1842|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*924A>G|||||924|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*924A>G|||||924|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*54A>G|||||54|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*54A>G|||||54|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1520:1:38:0,-8.54496,-133.284

+NC_045512.2	11919	.	C	T	48.6984	.	AB=0.219512;ABP=31.0276;AC=1;AF=0.5;AN=2;AO=9;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=22.5536;EPPR=72.4974;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=11.2132;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=342;QR=1214;RO=32;RPL=9;RPP=22.5536;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=22.5536;SAR=9;SRF=20;SRP=7.35324;SRR=12;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11654C>T|p.Ser3885Phe|11654/21291|11654/21291|3885/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11654C>T|p.Ser3885Phe|11654/13218|11654/13218|3885/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.77C>T|p.Ser26Phe|77/249|77/249|26/82||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.77C>T|p.Ser26Phe|77/249|77/249|26/82||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-173C>T|||||173|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-173C>T|||||173|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-767C>T|||||767|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-767C>T|||||767|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1106C>T|||||1106|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1106C>T|||||1106|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1523C>T|||||1523|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1523C>T|||||1523|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4318C>T|||||4318|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3365C>T|||||3365|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3365C>T|||||3365|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1865C>T|||||1865|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1865C>T|||||1865|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*947C>T|||||947|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*947C>T|||||947|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*77C>T|||||77|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*77C>T|||||77|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:41:32,9:32:1214:9:342:-18.7954,0,-97.2191

+NC_045512.2	11928	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=89.8692;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=51.0656;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1499;RO=40;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=20;SRP=3.0103;SRR=20;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11663G>A|p.Trp3888*|11663/21291|11663/21291|3888/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11663G>A|p.Trp3888*|11663/13218|11663/13218|3888/4405||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.86G>A|p.Trp29*|86/249|86/249|29/82||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.86G>A|p.Trp29*|86/249|86/249|29/82||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-164G>A|||||164|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-164G>A|||||164|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-758G>A|||||758|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-758G>A|||||758|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1097G>A|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1097G>A|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1514G>A|||||1514|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1514G>A|||||1514|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4309G>A|||||4309|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3374G>A|||||3374|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3374G>A|||||3374|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1874G>A|||||1874|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1874G>A|||||1874|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*956G>A|||||956|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*956G>A|||||956|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*86G>A|||||86|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*86G>A|||||86|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1499:1:38:0,-8.54496,-131.397

+NC_045512.2	11948	.	C	A	3.52281E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=61.9202;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=39.754;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1140;RO=31;RPL=1;RPP=5.18177;RPPR=14.8483;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=21;SRP=11.486;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11683C>A|p.His3895Asn|11683/21291|11683/21291|3895/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11683C>A|p.His3895Asn|11683/13218|11683/13218|3895/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.106C>A|p.His36Asn|106/249|106/249|36/82||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.106C>A|p.His36Asn|106/249|106/249|36/82||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-144C>A|||||144|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-144C>A|||||144|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-738C>A|||||738|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-738C>A|||||738|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1077C>A|||||1077|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1077C>A|||||1077|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1494C>A|||||1494|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1494C>A|||||1494|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4289C>A|||||4289|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3394C>A|||||3394|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3394C>A|||||3394|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1894C>A|||||1894|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1894C>A|||||1894|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*976C>A|||||976|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*976C>A|||||976|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*106C>A|||||106|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*106C>A|||||106|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1140:1:34:0,-6.23405,-99.5067

+NC_045512.2	11984	.	G	T	3.95377E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=3.0103;EPPR=3.9754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.8889;PAIRED=1;PAIREDR=0.972222;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1299;RO=36;RPL=0;RPP=7.35324;RPPR=81.1833;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11719G>T|p.Ala3907Ser|11719/21291|11719/21291|3907/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11719G>T|p.Ala3907Ser|11719/13218|11719/13218|3907/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.142G>T|p.Ala48Ser|142/249|142/249|48/82||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.142G>T|p.Ala48Ser|142/249|142/249|48/82||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-108G>T|||||108|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-108G>T|||||108|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-702G>T|||||702|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-702G>T|||||702|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1041G>T|||||1041|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1041G>T|||||1041|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1458G>T|||||1458|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1458G>T|||||1458|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4253G>T|||||4253|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3430G>T|||||3430|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3430G>T|||||3430|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1930G>T|||||1930|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1930G>T|||||1930|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1012G>T|||||1012|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1012G>T|||||1012|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*142G>T|||||142|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*142G>T|||||142|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:36,2:36:1299:2:76:0,-4.22433,-109.984

+NC_045512.2	12244	.	TGA	TA	1.54744E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1M1D1M;DP=40;DPB=39.3333;DPRA=0;EPP=7.35324;EPPR=8.7247;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.9438;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1417;RO=38;RPL=2;RPP=7.35324;RPPR=8.7247;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=10;SRP=21.525;SRR=28;TYPE=del;ANN=TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11980delG|p.Asp3994fs|11980/21291|11980/21291|3994/7096||,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11980delG|p.Asp3994fs|11980/13218|11980/13218|3994/4405||,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.154delG|p.Asp52fs|154/594|154/594|52/197||WARNING_TRANSCRIPT_NO_START_CODON,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.154delG|p.Asp52fs|154/594|154/594|52/197||WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-441delG|||||441|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-441delG|||||441|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-780delG|||||780|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-780delG|||||780|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1197delG|||||1197|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1197delG|||||1197|WARNING_TRANSCRIPT_NO_START_CODON,TA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3992delG|||||3992|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3691delG|||||3691|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3691delG|||||3691|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2191delG|||||2191|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2191delG|||||2191|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1273delG|||||1273|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1273delG|||||1273|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*403delG|||||403|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*403delG|||||403|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*154delG|||||154|WARNING_TRANSCRIPT_NO_START_CODON,TA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*154delG|||||154|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:38,2:38:1417:2:76:0,-4.82639,-120.603

+NC_045512.2	12259	.	A	T	2.26316E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=5.3706;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2448;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=874;RO=23;RPL=0;RPP=5.18177;RPPR=52.9542;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=5.3706;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11994A>T|p.Gln3998His|11994/21291|11994/21291|3998/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11994A>T|p.Gln3998His|11994/13218|11994/13218|3998/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.168A>T|p.Gln56His|168/594|168/594|56/197||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.168A>T|p.Gln56His|168/594|168/594|56/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-427A>T|||||427|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-427A>T|||||427|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-766A>T|||||766|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-766A>T|||||766|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1183A>T|||||1183|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1183A>T|||||1183|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3978A>T|||||3978|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3705A>T|||||3705|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3705A>T|||||3705|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2205A>T|||||2205|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2205A>T|||||2205|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1287A>T|||||1287|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1287A>T|||||1287|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*417A>T|||||417|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*417A>T|||||417|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*168A>T|||||168|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*168A>T|||||168|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:874:1:11:0,-6.12472,-77.8832

+NC_045512.2	12410	.	A	T	1.70989E-6	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=8.61041;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.7476;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=701;RO=19;RPL=2;RPP=7.35324;RPPR=44.2683;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=6;SRP=8.61041;SRR=13;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12145A>T|p.Ile4049Phe|12145/21291|12145/21291|4049/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12145A>T|p.Ile4049Phe|12145/13218|12145/13218|4049/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.319A>T|p.Ile107Phe|319/594|319/594|107/197||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.319A>T|p.Ile107Phe|319/594|319/594|107/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-276A>T|||||276|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-276A>T|||||276|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-615A>T|||||615|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-615A>T|||||615|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1032A>T|||||1032|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1032A>T|||||1032|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3827A>T|||||3827|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3856A>T|||||3856|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3856A>T|||||3856|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2356A>T|||||2356|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2356A>T|||||2356|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1438A>T|||||1438|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1438A>T|||||1438|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*568A>T|||||568|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*568A>T|||||568|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*319A>T|||||319|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*319A>T|||||319|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:701:2:75:-0.798713,0,-57.0966

+NC_045512.2	12419	.	G	T	2.15846E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=28;DPB=28;DPRA=0;EPP=5.18177;EPPR=61.6401;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.3424;PAIRED=1;PAIREDR=0.962963;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=968;RO=27;RPL=0;RPP=5.18177;RPPR=3.09072;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=3.09072;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12154G>T|p.Ala4052Ser|12154/21291|12154/21291|4052/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12154G>T|p.Ala4052Ser|12154/13218|12154/13218|4052/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.328G>T|p.Ala110Ser|328/594|328/594|110/197||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.328G>T|p.Ala110Ser|328/594|328/594|110/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-267G>T|||||267|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-267G>T|||||267|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-606G>T|||||606|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-606G>T|||||606|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1023G>T|||||1023|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1023G>T|||||1023|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3818G>T|||||3818|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3865G>T|||||3865|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3865G>T|||||3865|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2365G>T|||||2365|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2365G>T|||||2365|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1447G>T|||||1447|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1447G>T|||||1447|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*577G>T|||||577|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*577G>T|||||577|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*328G>T|||||328|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*328G>T|||||328|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:28:27,1:27:968:1:34:0,-5.02993,-84.0341

+NC_045512.2	12491	.	G	T	1.62542E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=46.4397;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=24.0087;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=760;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=46.4397;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12226G>T|p.Asp4076Tyr|12226/21291|12226/21291|4076/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12226G>T|p.Asp4076Tyr|12226/13218|12226/13218|4076/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.400G>T|p.Asp134Tyr|400/594|400/594|134/197||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.400G>T|p.Asp134Tyr|400/594|400/594|134/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-195G>T|||||195|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-195G>T|||||195|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-534G>T|||||534|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-534G>T|||||534|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-951G>T|||||951|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-951G>T|||||951|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3746G>T|||||3746|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3937G>T|||||3937|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3937G>T|||||3937|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2437G>T|||||2437|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2437G>T|||||2437|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1519G>T|||||1519|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1519G>T|||||1519|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*649G>T|||||649|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*649G>T|||||649|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*400G>T|||||400|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*400G>T|||||400|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:760:1:38:0,-2.52436,-64.9333

+NC_045512.2	12674	.	G	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.0103;EPPR=3.06598;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.8938;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1444;RO=39;RPL=2;RPP=7.35324;RPPR=87.6977;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=20;SRP=3.06598;SRR=19;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12409G>C|p.Val4137Leu|12409/21291|12409/21291|4137/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12409G>C|p.Val4137Leu|12409/13218|12409/13218|4137/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.583G>C|p.Val195Leu|583/594|583/594|195/197||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.583G>C|p.Val195Leu|583/594|583/594|195/197||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-12G>C|||||12|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-12G>C|||||12|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-351G>C|||||351|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-351G>C|||||351|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-768G>C|||||768|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-768G>C|||||768|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3563G>C|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4120G>C|||||4120|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4120G>C|||||4120|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2620G>C|||||2620|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2620G>C|||||2620|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1702G>C|||||1702|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1702G>C|||||1702|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*832G>C|||||832|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*832G>C|||||832|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*583G>C|||||583|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*583G>C|||||583|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:39,2:39:1444:2:76:0,-5.12742,-123.031

+NC_045512.2	12748	.	T	C	4.07431E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.18177;EPPR=65.983;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.1287;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1090;RO=29;RPL=0;RPP=5.18177;RPPR=12.0706;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=12.0706;SRR=20;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12483T>C|p.Thr4161Thr|12483/21291|12483/21291|4161/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12483T>C|p.Thr4161Thr|12483/13218|12483/13218|4161/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.63T>C|p.Thr21Thr|63/339|63/339|21/112||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.63T>C|p.Thr21Thr|63/339|63/339|21/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-277T>C|||||277|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-277T>C|||||277|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-694T>C|||||694|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-694T>C|||||694|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3489T>C|||||3489|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4194T>C|||||4194|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4194T>C|||||4194|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2694T>C|||||2694|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2694T>C|||||2694|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1776T>C|||||1776|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1776T>C|||||1776|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*906T>C|||||906|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*906T>C|||||906|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*657T>C|||||657|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*657T>C|||||657|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*63T>C|||||63|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*63T>C|||||63|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:30:29,1:29:1090:1:38:0,-5.23363,-94.6098

+NC_045512.2	12795	.	G	T	1.63938E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=5.18177;EPPR=51.9408;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=38.3995;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1092;RO=30;RPL=1;RPP=5.18177;RPPR=5.61607;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=10;SRP=10.2485;SRR=20;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12530G>T|p.Gly4177Val|12530/21291|12530/21291|4177/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12530G>T|p.Gly4177Val|12530/13218|12530/13218|4177/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.110G>T|p.Gly37Val|110/339|110/339|37/112||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.110G>T|p.Gly37Val|110/339|110/339|37/112||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-230G>T|||||230|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-230G>T|||||230|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-647G>T|||||647|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-647G>T|||||647|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3442G>T|||||3442|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4241G>T|||||4241|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4241G>T|||||4241|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2741G>T|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2741G>T|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1823G>T|||||1823|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1823G>T|||||1823|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*953G>T|||||953|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*953G>T|||||953|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*704G>T|||||704|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*704G>T|||||704|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*110G>T|||||110|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*110G>T|||||110|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:30,1:30:1092:1:34:0,-5.93302,-95.187

+NC_045512.2	12862	.	T	C	5.18713E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=18.6449;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.4565;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23;QR=751;RO=20;RPL=0;RPP=5.18177;RPPR=13.8677;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12597T>C|p.Ser4199Ser|12597/21291|12597/21291|4199/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12597T>C|p.Ser4199Ser|12597/13218|12597/13218|4199/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.177T>C|p.Ser59Ser|177/339|177/339|59/112||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.177T>C|p.Ser59Ser|177/339|177/339|59/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-163T>C|||||163|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-163T>C|||||163|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-580T>C|||||580|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-580T>C|||||580|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3375T>C|||||3375|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4308T>C|||||4308|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4308T>C|||||4308|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2808T>C|||||2808|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2808T>C|||||2808|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1890T>C|||||1890|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1890T>C|||||1890|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1020T>C|||||1020|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1020T>C|||||1020|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*771T>C|||||771|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*771T>C|||||771|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*177T>C|||||177|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*177T>C|||||177|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:751:1:23:0,-4.02172,-65.6201

+NC_045512.2	12864	.	A	T	2.12537E-6	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=22.325;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=717;RO=19;RPL=0;RPP=7.35324;RPPR=8.61041;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=9;SRP=3.12459;SRR=10;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12599A>T|p.Asp4200Val|12599/21291|12599/21291|4200/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12599A>T|p.Asp4200Val|12599/13218|12599/13218|4200/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.179A>T|p.Asp60Val|179/339|179/339|60/112||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.179A>T|p.Asp60Val|179/339|179/339|60/112||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-161A>T|||||161|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-161A>T|||||161|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-578A>T|||||578|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-578A>T|||||578|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3373A>T|||||3373|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4310A>T|||||4310|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4310A>T|||||4310|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2810A>T|||||2810|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2810A>T|||||2810|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1892A>T|||||1892|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1892A>T|||||1892|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1022A>T|||||1022|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1022A>T|||||1022|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*773A>T|||||773|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*773A>T|||||773|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*179A>T|||||179|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*179A>T|||||179|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:717:2:76:-0.893181,0,-58.5411

+NC_045512.2	13010	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=44;DPB=44;DPRA=0;EPP=5.18177;EPPR=34.5724;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=56.0711;PAIRED=0;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1481;RO=43;RPL=0;RPP=5.18177;RPPR=3.46479;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=25.2805;SRR=11;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12745A>C|p.Thr4249Pro|12745/21291|12745/21291|4249/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12745A>C|p.Thr4249Pro|12745/13218|12745/13218|4249/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.325A>C|p.Thr109Pro|325/339|325/339|109/112||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.325A>C|p.Thr109Pro|325/339|325/339|109/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-15A>C|||||15|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-15A>C|||||15|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-432A>C|||||432|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-432A>C|||||432|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3227A>C|||||3227|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4456A>C|||||4456|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4456A>C|||||4456|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2956A>C|||||2956|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2956A>C|||||2956|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2038A>C|||||2038|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2038A>C|||||2038|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1168A>C|||||1168|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1168A>C|||||1168|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*919A>C|||||919|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*919A>C|||||919|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*325A>C|||||325|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*325A>C|||||325|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:44:43,1:43:1481:1:34:0,-9.84641,-130.176

+NC_045512.2	13012	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=66.97;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.4981;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1565;RO=44;RPL=0;RPP=5.18177;RPPR=12.6832;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=33;SRP=26.8965;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12747A>C|p.Thr4249Thr|12747/21291|12747/21291|4249/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12747A>C|p.Thr4249Thr|12747/13218|12747/13218|4249/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.327A>C|p.Thr109Thr|327/339|327/339|109/112||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.327A>C|p.Thr109Thr|327/339|327/339|109/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-13A>C|||||13|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-13A>C|||||13|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-430A>C|||||430|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-430A>C|||||430|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3225A>C|||||3225|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4458A>C|||||4458|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4458A>C|||||4458|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2958A>C|||||2958|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2958A>C|||||2958|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2040A>C|||||2040|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2040A>C|||||2040|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1170A>C|||||1170|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1170A>C|||||1170|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*921A>C|||||921|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*921A>C|||||921|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*327A>C|||||327|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*327A>C|||||327|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1565:1:12:0,-12.3464,-139.935

+NC_045512.2	13015	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=48;DPB=48;DPRA=0;EPP=5.18177;EPPR=88.4369;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=62.2188;PAIRED=1;PAIREDR=0.957447;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1739;RO=47;RPL=0;RPP=5.18177;RPPR=23.3852;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=31.8863;SRR=11;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12750A>C|p.Val4250Val|12750/21291|12750/21291|4250/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12750A>C|p.Val4250Val|12750/13218|12750/13218|4250/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding|1/1|c.330A>C|p.Val110Val|330/339|330/339|110/112||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding|1/1|c.330A>C|p.Val110Val|330/339|330/339|110/112||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-10A>C|||||10|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-10A>C|||||10|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-427A>C|||||427|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-427A>C|||||427|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3222A>C|||||3222|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4461A>C|||||4461|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4461A>C|||||4461|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2961A>C|||||2961|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2961A>C|||||2961|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2043A>C|||||2043|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2043A>C|||||2043|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1173A>C|||||1173|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1173A>C|||||1173|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*924A>C|||||924|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*924A>C|||||924|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*330A>C|||||330|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*330A>C|||||330|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:48:47,1:47:1739:1:31:0,-11.35,-153.682

+NC_045512.2	13022	.	CAAGC	CAAAGC	6.14782E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=47;DPB=47.2;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2468;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1746;RO=46;RPL=0;RPP=5.18177;RPPR=30.2009;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=30.2009;SRR=11;TYPE=ins;ANN=CAAAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12759dupA|p.Ala4254fs|12760/21291|12760/21291|4254/7096||,CAAAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12759dupA|p.Ala4254fs|12760/13218|12760/13218|4254/4405||,CAAAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.-1dupA|p.Ala1fs|1/417|1/417|1/138||WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.-1dupA|p.Ala1fs|1/417|1/417|1/138||WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-418dupA|||||417|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-418dupA|||||417|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3213dupA|||||3212|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4470dupA|||||4471|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4470dupA|||||4471|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2970dupA|||||2971|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2970dupA|||||2971|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2052dupA|||||2053|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2052dupA|||||2053|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1182dupA|||||1183|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1182dupA|||||1183|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*933dupA|||||934|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*933dupA|||||934|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*339dupA|||||340|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*339dupA|||||340|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.339dupA|||||1|WARNING_TRANSCRIPT_NO_START_CODON,CAAAGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.339dupA|||||1|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:47:46,1:46:1746:1:38:0,-10.3511,-153.61

+NC_045512.2	13050	.	C	T	6.14782E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.18177;EPPR=102.898;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.2468;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1721;RO=46;RPL=0;RPP=5.18177;RPPR=30.2009;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=30.2009;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12785C>T|p.Ala4262Val|12785/21291|12785/21291|4262/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12785C>T|p.Ala4262Val|12785/13218|12785/13218|4262/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.26C>T|p.Ala9Val|26/417|26/417|9/138||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.26C>T|p.Ala9Val|26/417|26/417|9/138||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-392C>T|||||392|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-392C>T|||||392|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3187C>T|||||3187|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4990C>T|||||4990|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4496C>T|||||4496|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4496C>T|||||4496|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2996C>T|||||2996|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2996C>T|||||2996|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2078C>T|||||2078|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2078C>T|||||2078|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1208C>T|||||1208|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1208C>T|||||1208|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*959C>T|||||959|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*959C>T|||||959|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*365C>T|||||365|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*365C>T|||||365|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*26C>T|||||26|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*26C>T|||||26|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:47:46,1:46:1721:1:38:0,-10.3511,-151.356

+NC_045512.2	13088	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=5.18177;EPPR=8.46682;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=103.089;PAIRED=1;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2892;RO=78;RPL=1;RPP=5.18177;RPPR=96.662;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=4.01252;SRR=42;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12823G>T|p.Asp4275Tyr|12823/21291|12823/21291|4275/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12823G>T|p.Asp4275Tyr|12823/13218|12823/13218|4275/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.64G>T|p.Asp22Tyr|64/417|64/417|22/138||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.64G>T|p.Asp22Tyr|64/417|64/417|22/138||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-354G>T|||||354|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-354G>T|||||354|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3149G>T|||||3149|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4952G>T|||||4952|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4534G>T|||||4534|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4534G>T|||||4534|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3034G>T|||||3034|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3034G>T|||||3034|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2116G>T|||||2116|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2116G>T|||||2116|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1246G>T|||||1246|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1246G>T|||||1246|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*997G>T|||||997|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*997G>T|||||997|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*403G>T|||||403|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*403G>T|||||403|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*64G>T|||||64|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*64G>T|||||64|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:79:78,1:78:2892:1:38:0,-19.9841,-256.684

+NC_045512.2	13090	.	T	A	8.10661E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=3.0103;EPPR=9.35551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=92.4668;PAIRED=1;PAIREDR=0.961039;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=2841;RO=77;RPL=0;RPP=7.35324;RPPR=88.3181;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=35;SRP=4.39215;SRR=42;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12825T>A|p.Asp4275Glu|12825/21291|12825/21291|4275/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12825T>A|p.Asp4275Glu|12825/13218|12825/13218|4275/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.66T>A|p.Asp22Glu|66/417|66/417|22/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.66T>A|p.Asp22Glu|66/417|66/417|22/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-352T>A|||||352|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-352T>A|||||352|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3147T>A|||||3147|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4950T>A|||||4950|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4536T>A|||||4536|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4536T>A|||||4536|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3036T>A|||||3036|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3036T>A|||||3036|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2118T>A|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2118T>A|||||2118|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1248T>A|||||1248|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1248T>A|||||1248|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*999T>A|||||999|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*999T>A|||||999|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*405T>A|||||405|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*405T>A|||||405|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*66T>A|||||66|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*66T>A|||||66|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:79:77,2:77:2841:2:75:0,-16.661,-248.778

+NC_045512.2	13118	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=3.0103;EPPR=3.04177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=81.5914;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=2581;RO=69;RPL=0;RPP=7.35324;RPPR=152.842;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=35;SRP=3.04177;SRR=34;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12853G>T|p.Ala4285Ser|12853/21291|12853/21291|4285/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12853G>T|p.Ala4285Ser|12853/13218|12853/13218|4285/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.94G>T|p.Ala32Ser|94/417|94/417|32/138||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.94G>T|p.Ala32Ser|94/417|94/417|32/138||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-324G>T|||||324|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-324G>T|||||324|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3119G>T|||||3119|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4922G>T|||||4922|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4564G>T|||||4564|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4564G>T|||||4564|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3064G>T|||||3064|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3064G>T|||||3064|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2146G>T|||||2146|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2146G>T|||||2146|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1276G>T|||||1276|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1276G>T|||||1276|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1027G>T|||||1027|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1027G>T|||||1027|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*433G>T|||||433|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*433G>T|||||433|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*94G>T|||||94|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*94G>T|||||94|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:71:69,2:69:2581:2:75:0,-14.2528,-225.389

+NC_045512.2	13168	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=157.185;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=98.3068;PAIRED=0;PAIREDR=0.957746;PAO=0;PQA=0;PQR=0;PRO=0;QA=17;QR=2691;RO=71;RPL=0;RPP=5.18177;RPPR=3.04088;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12903C>A|p.His4301Gln|12903/21291|12903/21291|4301/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12903C>A|p.His4301Gln|12903/13218|12903/13218|4301/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.144C>A|p.His48Gln|144/417|144/417|48/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.144C>A|p.His48Gln|144/417|144/417|48/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-274C>A|||||274|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-274C>A|||||274|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3069C>A|||||3069|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4872C>A|||||4872|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4614C>A|||||4614|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4614C>A|||||4614|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3114C>A|||||3114|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3114C>A|||||3114|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2196C>A|||||2196|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2196C>A|||||2196|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1326C>A|||||1326|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1326C>A|||||1326|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1077C>A|||||1077|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1077C>A|||||1077|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*483C>A|||||483|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*483C>A|||||483|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*144C>A|||||144|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*144C>A|||||144|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:72:71,1:71:2691:1:17:0,-19.9742,-240.697

+NC_045512.2	13174	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=157.185;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6883;PAIRED=0;PAIREDR=0.957746;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2694;RO=71;RPL=0;RPP=5.18177;RPPR=3.04088;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12909T>G|p.Gly4303Gly|12909/21291|12909/21291|4303/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12909T>G|p.Gly4303Gly|12909/13218|12909/13218|4303/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.150T>G|p.Gly50Gly|150/417|150/417|50/138||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.150T>G|p.Gly50Gly|150/417|150/417|50/138||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-268T>G|||||268|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-268T>G|||||268|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3063T>G|||||3063|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4866T>G|||||4866|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4620T>G|||||4620|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4620T>G|||||4620|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3120T>G|||||3120|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3120T>G|||||3120|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2202T>G|||||2202|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2202T>G|||||2202|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1332T>G|||||1332|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1332T>G|||||1332|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1083T>G|||||1083|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1083T>G|||||1083|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*489T>G|||||489|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*489T>G|||||489|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*150T>G|||||150|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*150T>G|||||150|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:72:71,1:71:2694:1:11:0,-20.5742,-241.567

+NC_045512.2	13190	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=157.185;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6883;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2678;RO=71;RPL=1;RPP=5.18177;RPPR=3.04088;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.04088;SRR=36;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12925A>T|p.Thr4309Ser|12925/21291|12925/21291|4309/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12925A>T|p.Thr4309Ser|12925/13218|12925/13218|4309/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.166A>T|p.Thr56Ser|166/417|166/417|56/138||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.166A>T|p.Thr56Ser|166/417|166/417|56/138||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-252A>T|||||252|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-252A>T|||||252|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3047A>T|||||3047|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4850A>T|||||4850|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4636A>T|||||4636|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4636A>T|||||4636|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3136A>T|||||3136|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3136A>T|||||3136|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2218A>T|||||2218|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2218A>T|||||2218|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1348A>T|||||1348|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1348A>T|||||1348|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1099A>T|||||1099|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1099A>T|||||1099|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*505A>T|||||505|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*505A>T|||||505|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*166A>T|||||166|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*166A>T|||||166|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:72:71,1:71:2678:1:11:0,-20.5742,-240.128

+NC_045512.2	13232	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=109.474;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=93.7066;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=37;QR=2685;RO=71;RPL=1;RPP=5.18177;RPPR=8.17902;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12967G>A|p.Gly4323Ser|12967/21291|12967/21291|4323/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12967G>A|p.Gly4323Ser|12967/13218|12967/13218|4323/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.208G>A|p.Gly70Ser|208/417|208/417|70/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.208G>A|p.Gly70Ser|208/417|208/417|70/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-210G>A|||||210|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-210G>A|||||210|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3005G>A|||||3005|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4808G>A|||||4808|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4678G>A|||||4678|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4678G>A|||||4678|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3178G>A|||||3178|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3178G>A|||||3178|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2260G>A|||||2260|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2260G>A|||||2260|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1390G>A|||||1390|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1390G>A|||||1390|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1141G>A|||||1141|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1141G>A|||||1141|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*547G>A|||||547|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*547G>A|||||547|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*208G>A|||||208|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*208G>A|||||208|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:72:71,1:71:2685:1:37:0,-17.9763,-238.162

+NC_045512.2	13235	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=16.4979;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=95.3144;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=2650;RO=71;RPL=1;RPP=5.18177;RPPR=82.5596;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=36;SRP=3.04088;SRR=35;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12970G>A|p.Ala4324Thr|12970/21291|12970/21291|4324/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12970G>A|p.Ala4324Thr|12970/13218|12970/13218|4324/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.211G>A|p.Ala71Thr|211/417|211/417|71/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.211G>A|p.Ala71Thr|211/417|211/417|71/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-207G>A|||||207|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-207G>A|||||207|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3002G>A|||||3002|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4805G>A|||||4805|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4681G>A|||||4681|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4681G>A|||||4681|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3181G>A|||||3181|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3181G>A|||||3181|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2263G>A|||||2263|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2263G>A|||||2263|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1393G>A|||||1393|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1393G>A|||||1393|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1144G>A|||||1144|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1144G>A|||||1144|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*550G>A|||||550|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*550G>A|||||550|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*211G>A|||||211|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*211G>A|||||211|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:72:71,1:71:2650:1:30:0,-18.6746,-235.707

+NC_045512.2	13238	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=72;DPB=72;DPRA=0;EPP=5.18177;EPPR=4.50892;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=99.6883;PAIRED=1;PAIREDR=0.943662;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2680;RO=71;RPL=1;RPP=5.18177;RPPR=124.399;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.04088;SRR=36;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12973T>A|p.Ser4325Thr|12973/21291|12973/21291|4325/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12973T>A|p.Ser4325Thr|12973/13218|12973/13218|4325/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.214T>A|p.Ser72Thr|214/417|214/417|72/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.214T>A|p.Ser72Thr|214/417|214/417|72/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-204T>A|||||204|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-204T>A|||||204|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2999T>A|||||2999|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4802T>A|||||4802|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4684T>A|||||4684|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4684T>A|||||4684|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3184T>A|||||3184|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3184T>A|||||3184|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2266T>A|||||2266|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2266T>A|||||2266|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1396T>A|||||1396|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1396T>A|||||1396|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1147T>A|||||1147|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1147T>A|||||1147|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*553T>A|||||553|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*553T>A|||||553|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*214T>A|||||214|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*214T>A|||||214|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:72:71,1:71:2680:1:11:0,-20.5742,-240.31

+NC_045512.2	13326	.	CAACT	CAAACT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1I4M;DP=40;DPB=40.2;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.137;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1436;RO=38;RPL=0;RPP=5.18177;RPPR=69.0688;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=2;SRP=69.0688;SRR=36;TYPE=ins;ANN=CAAACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13063dupA|p.Thr4355fs|13064/21291|13064/21291|4355/7096||,CAAACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.13063dupA|p.Thr4355fs|13064/13218|13064/13218|4355/4405||,CAAACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.304dupA|p.Thr102fs|305/417|305/417|102/138||WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.304dupA|p.Thr102fs|305/417|305/417|102/138||WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-114dupA|||||113|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-114dupA|||||113|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2909dupA|||||2908|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4712dupA|||||4711|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4774dupA|||||4775|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4774dupA|||||4775|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3274dupA|||||3275|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3274dupA|||||3275|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2356dupA|||||2357|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2356dupA|||||2357|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1486dupA|||||1487|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1486dupA|||||1487|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1237dupA|||||1238|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1237dupA|||||1238|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*643dupA|||||644|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*643dupA|||||644|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*304dupA|||||305|WARNING_TRANSCRIPT_NO_START_CODON,CAAACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*304dupA|||||305|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:38,1:38:1436:1:38:0,-8.28774,-125.764

+NC_045512.2	13384	.	C	G	3.19931E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=5.18177;EPPR=55.1256;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2968;PAIRED=1;PAIREDR=0.916667;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=842;RO=24;RPL=1;RPP=5.18177;RPPR=26.1727;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=26.1727;SRR=20;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13119C>G|p.Cys4373Trp|13119/21291|13119/21291|4373/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.13119C>G|p.Cys4373Trp|13119/13218|13119/13218|4373/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.360C>G|p.Cys120Trp|360/417|360/417|120/138||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.360C>G|p.Cys120Trp|360/417|360/417|120/138||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-58C>G|||||58|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-58C>G|||||58|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2853C>G|||||2853|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4656C>G|||||4656|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4830C>G|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4830C>G|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3330C>G|||||3330|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3330C>G|||||3330|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2412C>G|||||2412|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2412C>G|||||2412|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1542C>G|||||1542|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1542C>G|||||1542|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1293C>G|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1293C>G|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*699C>G|||||699|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*699C>G|||||699|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*360C>G|||||360|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*360C>G|||||360|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:25:24,1:24:842:1:34:0,-4.12684,-72.6983

+NC_045512.2	13385	.	G	C	2.47418E-10	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=20;DPB=20;DPRA=0;EPP=5.18177;EPPR=44.2683;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=23.5885;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=674;RO=19;RPL=1;RPP=5.18177;RPPR=16.8392;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=4;SRP=16.8392;SRR=15;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.13120G>C|p.Gly4374Arg|13120/21291|13120/21291|4374/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.13120G>C|p.Gly4374Arg|13120/13218|13120/13218|4374/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.361G>C|p.Gly121Arg|361/417|361/417|121/138||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.361G>C|p.Gly121Arg|361/417|361/417|121/138||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-57G>C|||||57|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-57G>C|||||57|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2852G>C|||||2852|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4655G>C|||||4655|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4831G>C|||||4831|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4831G>C|||||4831|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3331G>C|||||3331|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3331G>C|||||3331|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2413G>C|||||2413|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2413G>C|||||2413|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1543G>C|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1543G>C|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1294G>C|||||1294|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1294G>C|||||1294|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*700G>C|||||700|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*700G>C|||||700|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*361G>C|||||361|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*361G>C|||||361|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:20:19,1:19:674:1:34:0,-2.62169,-57.5867

+NC_045512.2	13605	.	C	A	7.3683E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=5.18177;EPPR=58.6;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=57.046;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1403;RO=40;RPL=0;RPP=5.18177;RPPR=34.2795;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=36;SRP=58.6;SRR=4;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13341C>A|p.Arg4447Arg|13341/21291|13341/21291|4447/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.165C>A|p.Arg55Arg|165/2796|165/2796|55/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2632C>A|||||2632|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4435C>A|||||4435|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*122C>A|||||122|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3551C>A|||||3551|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3551C>A|||||3551|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2633C>A|||||2633|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2633C>A|||||2633|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1763C>A|||||1763|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1763C>A|||||1763|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1514C>A|||||1514|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1514C>A|||||1514|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*920C>A|||||920|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*920C>A|||||920|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*581C>A|||||581|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*581C>A|||||581|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*164C>A|||||164|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*164C>A|||||164|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*125C>A|||||125|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:41:40,1:40:1403:1:12:0,-11.1422,-125.355

+NC_045512.2	13690	.	G	T	1.34405E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9749;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2274;RO=61;RPL=0;RPP=5.18177;RPPR=135.47;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13426G>T|p.Glu4476*|13426/21291|13426/21291|4476/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.250G>T|p.Glu84*|250/2796|250/2796|84/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2547G>T|||||2547|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4350G>T|||||4350|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*207G>T|||||207|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3636G>T|||||3636|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3636G>T|||||3636|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2718G>T|||||2718|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2718G>T|||||2718|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1848G>T|||||1848|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1848G>T|||||1848|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1599G>T|||||1599|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1599G>T|||||1599|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1005G>T|||||1005|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1005G>T|||||1005|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*666G>T|||||666|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*666G>T|||||666|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*249G>T|||||249|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*249G>T|||||249|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*210G>T|||||210|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2274:1:11:0,-17.5639,-203.8

+NC_045512.2	13724	.	C	T	1.34405E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9749;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2292;RO=61;RPL=0;RPP=5.18177;RPPR=135.47;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13460C>T|p.Ala4487Val|13460/21291|13460/21291|4487/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.284C>T|p.Ala95Val|284/2796|284/2796|95/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2513C>T|||||2513|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4316C>T|||||4316|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*241C>T|||||241|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3670C>T|||||3670|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3670C>T|||||3670|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2752C>T|||||2752|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2752C>T|||||2752|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1882C>T|||||1882|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1882C>T|||||1882|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1633C>T|||||1633|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1633C>T|||||1633|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1039C>T|||||1039|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1039C>T|||||1039|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*700C>T|||||700|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*700C>T|||||700|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*283C>T|||||283|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*283C>T|||||283|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*244C>T|||||244|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2292:1:11:0,-17.5639,-205.418

+NC_045512.2	13748	.	A	T	1.34405E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.0459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=85.9749;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=2297;RO=61;RPL=0;RPP=5.18177;RPPR=118.668;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13484A>T|p.Lys4495Met|13484/21291|13484/21291|4495/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.308A>T|p.Lys103Met|308/2796|308/2796|103/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2489A>T|||||2489|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4292A>T|||||4292|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*265A>T|||||265|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3694A>T|||||3694|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3694A>T|||||3694|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2776A>T|||||2776|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2776A>T|||||2776|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1906A>T|||||1906|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1906A>T|||||1906|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1657A>T|||||1657|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1657A>T|||||1657|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1063A>T|||||1063|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1063A>T|||||1063|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*724A>T|||||724|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*724A>T|||||724|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*307A>T|||||307|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*307A>T|||||307|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*268A>T|||||268|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2297:1:11:0,-17.5639,-205.865

+NC_045512.2	13796	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=126.927;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.7642;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=2317;RO=61;RPL=1;RPP=5.18177;RPPR=3.90025;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=32;SRP=3.33068;SRR=29;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13532T>C|p.Leu4511Pro|13532/21291|13532/21291|4511/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.356T>C|p.Leu119Pro|356/2796|356/2796|119/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2441T>C|||||2441|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4244T>C|||||4244|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*313T>C|||||313|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3742T>C|||||3742|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3742T>C|||||3742|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2824T>C|||||2824|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2824T>C|||||2824|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1954T>C|||||1954|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1954T>C|||||1954|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1705T>C|||||1705|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1705T>C|||||1705|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1111T>C|||||1111|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1111T>C|||||1111|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*772T>C|||||772|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*772T>C|||||772|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*355T>C|||||355|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*355T>C|||||355|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*316T>C|||||316|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2317:1:38:0,-14.8666,-204.963

+NC_045512.2	13835	.	G	A	3.76714E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.90025;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=80.2224;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=36;QR=2306;RO=61;RPL=1;RPP=5.18177;RPPR=135.47;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.90025;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13571G>A|p.Arg4524Lys|13571/21291|13571/21291|4524/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.395G>A|p.Arg132Lys|395/2796|395/2796|132/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2402G>A|||||2402|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4205G>A|||||4205|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*352G>A|||||352|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3781G>A|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3781G>A|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2863G>A|||||2863|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2863G>A|||||2863|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1993G>A|||||1993|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1993G>A|||||1993|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1744G>A|||||1744|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1744G>A|||||1744|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1150G>A|||||1150|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1150G>A|||||1150|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*811G>A|||||811|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*811G>A|||||811|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*394G>A|||||394|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*394G>A|||||394|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*355G>A|||||355|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2306:1:36:0,-15.0656,-204.175

+NC_045512.2	13932	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.5097;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1404;RO=37;RPL=1;RPP=5.18177;RPPR=24.1968;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=24.1968;SRR=28;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13668T>G|p.Asp4556Glu|13668/21291|13668/21291|4556/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.492T>G|p.Asp164Glu|492/2796|492/2796|164/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2305T>G|||||2305|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4108T>G|||||4108|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*449T>G|||||449|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3878T>G|||||3878|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3878T>G|||||3878|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2960T>G|||||2960|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2960T>G|||||2960|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2090T>G|||||2090|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2090T>G|||||2090|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1841T>G|||||1841|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1841T>G|||||1841|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1247T>G|||||1247|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1247T>G|||||1247|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*908T>G|||||908|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*908T>G|||||908|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*491T>G|||||491|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*491T>G|||||491|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*452T>G|||||452|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1404:1:27:0,-8.73936,-123.949

+NC_045512.2	13971	.	CTTAG	CTAG,CTTG	3.76391E-14	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=2,1;CIGAR=1M1D3M,3M1D1M;DP=38;DPB=37.4;DPRA=0,0;EPP=7.35324,5.18177;EPPR=70.5741;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=37.8173;PAIRED=0.5,1;PAIREDR=0.971429;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,38;QR=1299;RO=35;RPL=2,1;RPP=7.35324,5.18177;RPPR=16.9698;RPR=0,0;RUN=1,1;SAF=0,0;SAP=7.35324,5.18177;SAR=2,1;SRF=9;SRP=20.9405;SRR=26;TYPE=del,del;ANN=CTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13709delT|p.Leu4570fs|13709/21291|13709/21291|4570/7096||,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13710delA|p.Gly4571fs|13710/21291|13710/21291|4570/7096||,CTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.533delT|p.Leu178fs|533/2796|533/2796|178/931||WARNING_TRANSCRIPT_NO_START_CODON,CTTG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.534delA|p.Gly179fs|534/2796|534/2796|178/931||WARNING_TRANSCRIPT_NO_START_CODON,CTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2264delT|||||2264|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2263delA|||||2263|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4067delT|||||4067|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4066delA|||||4066|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*490delT|||||490|,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*491delA|||||491|,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3919delT|||||3919|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3920delA|||||3920|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3919delT|||||3919|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3920delA|||||3920|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3001delT|||||3001|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3002delA|||||3002|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3001delT|||||3001|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3002delA|||||3002|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2131delT|||||2131|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2132delA|||||2132|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2131delT|||||2131|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2132delA|||||2132|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1882delT|||||1882|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1883delA|||||1883|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1882delT|||||1882|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1883delA|||||1883|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1288delT|||||1288|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1289delA|||||1289|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1288delT|||||1288|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1289delA|||||1289|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*949delT|||||949|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*950delA|||||950|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*949delT|||||949|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*950delA|||||950|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*532delT|||||532|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*533delA|||||533|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*532delT|||||532|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*533delA|||||533|WARNING_TRANSCRIPT_NO_START_CODON,CTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*493delT|||||493|WARNING_TRANSCRIPT_NO_START_CODON,CTTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*494delA|||||494|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:35,2,1:35:1299:2,1:76,38:0,-4.30303,-109.993,-7.41954,-107.478,-113.411

+NC_045512.2	13983	.	T	G	3.56286E-9	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=18;DPB=18;DPRA=0;EPP=5.18177;EPPR=31.7504;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=20.9213;PAIRED=1;PAIREDR=0.882353;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=616;RO=17;RPL=1;RPP=5.18177;RPPR=4.1599;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.13803;SRR=8;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13719T>G|p.Arg4573Arg|13719/21291|13719/21291|4573/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.543T>G|p.Arg181Arg|543/2796|543/2796|181/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2254T>G|||||2254|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4057T>G|||||4057|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*500T>G|||||500|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3929T>G|||||3929|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3929T>G|||||3929|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3011T>G|||||3011|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3011T>G|||||3011|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2141T>G|||||2141|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2141T>G|||||2141|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1892T>G|||||1892|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1892T>G|||||1892|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1298T>G|||||1298|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1298T>G|||||1298|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*959T>G|||||959|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*959T>G|||||959|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*542T>G|||||542|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*542T>G|||||542|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*503T>G|||||503|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:18:17,1:17:616:1:34:0,-2.01963,-52.3727

+NC_045512.2	14038	.	G	A	3.36415E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=5.18177;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=30.2194;PAIRED=1;PAIREDR=0.95;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=732;RO=20;RPL=0;RPP=5.18177;RPPR=46.4397;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=9;SRP=3.44459;SRR=11;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13774G>A|p.Gly4592Ser|13774/21291|13774/21291|4592/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.598G>A|p.Gly200Ser|598/2796|598/2796|200/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2199G>A|||||2199|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4002G>A|||||4002|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*555G>A|||||555|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3984G>A|||||3984|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3984G>A|||||3984|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3066G>A|||||3066|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3066G>A|||||3066|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2196G>A|||||2196|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2196G>A|||||2196|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1947G>A|||||1947|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1947G>A|||||1947|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1353G>A|||||1353|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1353G>A|||||1353|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1014G>A|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1014G>A|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*597G>A|||||597|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*597G>A|||||597|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*558G>A|||||558|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:21:20,1:20:732:1:11:0,-5.22163,-65.104

+NC_045512.2	14176	.	A	G	2.12537E-6	.	AB=0.0952381;ABP=32.8939;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=21;DPB=21;DPRA=0;EPP=3.0103;EPPR=4.03889;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=14.5301;PAIRED=1;PAIREDR=0.947368;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=710;RO=19;RPL=2;RPP=7.35324;RPPR=44.2683;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=8;SRP=4.03889;SRR=11;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13912A>G|p.Thr4638Ala|13912/21291|13912/21291|4638/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.736A>G|p.Thr246Ala|736/2796|736/2796|246/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2061A>G|||||2061|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3864A>G|||||3864|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*693A>G|||||693|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4122A>G|||||4122|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4122A>G|||||4122|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3204A>G|||||3204|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3204A>G|||||3204|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2334A>G|||||2334|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2334A>G|||||2334|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2085A>G|||||2085|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2085A>G|||||2085|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1491A>G|||||1491|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1491A>G|||||1491|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1152A>G|||||1152|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1152A>G|||||1152|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*735A>G|||||735|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*735A>G|||||735|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*696A>G|||||696|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:21:19,2:19:710:2:76:-0.893181,0,-57.9105

+NC_045512.2	14269	.	G	A	2.90829E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.18177;EPPR=81.1833;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.623;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1368;RO=36;RPL=1;RPP=5.18177;RPPR=18.4519;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=18.4519;SRR=10;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14005G>A|p.Glu4669Lys|14005/21291|14005/21291|4669/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.829G>A|p.Glu277Lys|829/2796|829/2796|277/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1968G>A|||||1968|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3771G>A|||||3771|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*786G>A|||||786|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4215G>A|||||4215|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4215G>A|||||4215|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3297G>A|||||3297|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3297G>A|||||3297|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2427G>A|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2427G>A|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2178G>A|||||2178|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2178G>A|||||2178|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1584G>A|||||1584|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1584G>A|||||1584|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1245G>A|||||1245|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1245G>A|||||1245|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*828G>A|||||828|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*828G>A|||||828|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*789G>A|||||789|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:37:36,1:36:1368:1:38:0,-7.34084,-119.614

+NC_045512.2	14290	.	G	T	6.2985E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=74.9036;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.9827;PAIRED=1;PAIREDR=0.945946;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1383;RO=37;RPL=1;RPP=5.18177;RPPR=19.9713;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=26;SRP=16.2152;SRR=11;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14026G>T|p.Asp4676Tyr|14026/21291|14026/21291|4676/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.850G>T|p.Asp284Tyr|850/2796|850/2796|284/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1947G>T|||||1947|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3750G>T|||||3750|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*807G>T|||||807|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4236G>T|||||4236|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4236G>T|||||4236|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3318G>T|||||3318|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3318G>T|||||3318|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2448G>T|||||2448|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2448G>T|||||2448|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2199G>T|||||2199|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2199G>T|||||2199|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1605G>T|||||1605|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1605G>T|||||1605|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1266G>T|||||1266|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1266G>T|||||1266|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*849G>T|||||849|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*849G>T|||||849|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*810G>T|||||810|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1383:1:38:0,-7.64187,-120.964

+NC_045512.2	14327	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=3.0103;EPPR=3.19126;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1782;RO=48;RPL=0;RPP=7.35324;RPPR=107.241;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14063C>T|p.Pro4688Leu|14063/21291|14063/21291|4688/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.887C>T|p.Pro296Leu|887/2796|887/2796|296/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1910C>T|||||1910|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3713C>T|||||3713|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*844C>T|||||844|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4273C>T|||||4273|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4273C>T|||||4273|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3355C>T|||||3355|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3355C>T|||||3355|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2485C>T|||||2485|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2485C>T|||||2485|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2236C>T|||||2236|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2236C>T|||||2236|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1642C>T|||||1642|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1642C>T|||||1642|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1303C>T|||||1303|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1303C>T|||||1303|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*886C>T|||||886|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*886C>T|||||886|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*847C>T|||||847|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:50:48,2:48:1782:2:76:0,-7.83669,-153.432

+NC_045512.2	14407	.	CCTACAAGT	CT,CTTACAAGT	1314.95	.	AB=0.28,0.72;ABP=24.0302,24.0302;AC=1,1;AF=0.5,0.5;AN=2;AO=14,36;CIGAR=1M7D1M,1M1X7M;DP=50;DPB=39.1111;DPRA=0,0;EPP=33.4109,81.1833;EPPR=0;GTI=0;LEN=7,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=48.6802;PAIRED=0.928571,0.944444;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=518,1367;QR=0;RO=0;RPL=8,18;RPP=3.63072,3.0103;RPPR=0;RPR=6,18;RUN=1,1;SAF=8,18;SAP=3.63072,3.0103;SAR=6,18;SRF=0;SRP=0;SRR=0;TYPE=del,snp;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144_14150delCTACAAG|p.Pro4715fs|14144/21291|14144/21291|4715/7096||,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.968_974delCTACAAG|p.Pro323fs|968/2796|968/2796|323/931||WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144C>T|p.Pro4715Leu|14144/21291|14144/21291|4715/7096||,CTTACAAGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.968C>T|p.Pro323Leu|968/2796|968/2796|323/931||WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1829C>T|||||1829|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1829_-1823delCTACAAG|||||1829|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3632C>T|||||3632|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3632_-3626delCTACAAG|||||3632|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*925C>T|||||925|,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*925_*931delCTACAAG|||||925|,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4354C>T|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4354_*4360delCTACAAG|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4354C>T|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4354_*4360delCTACAAG|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3436C>T|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3436_*3442delCTACAAG|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3436C>T|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3436_*3442delCTACAAG|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2566C>T|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2566_*2572delCTACAAG|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2566C>T|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2566_*2572delCTACAAG|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2317C>T|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2317_*2323delCTACAAG|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2317C>T|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2317_*2323delCTACAAG|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1723C>T|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1723_*1729delCTACAAG|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1723C>T|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1723_*1729delCTACAAG|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1384C>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1384_*1390delCTACAAG|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1384C>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1384_*1390delCTACAAG|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*967_*973delCTACAAG|||||967|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*967_*973delCTACAAG|||||967|WARNING_TRANSCRIPT_NO_START_CODON,CTTACAAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*928C>T|||||928|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*928_*934delCTACAAG|||||928|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	1/2:50:0,14,36:0:0:14,36:518,1367:-154.858,-112.484,-108.27,-42.7461,0,-31.9091

+NC_045512.2	14435	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=7.35324;EPPR=107.241;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1765;RO=48;RPL=1;RPP=3.0103;RPPR=3.19126;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14171A>T|p.Lys4724Ile|14171/21291|14171/21291|4724/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.995A>T|p.Lys332Ile|995/2796|995/2796|332/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1802A>T|||||1802|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3605A>T|||||3605|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*952A>T|||||952|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4381A>T|||||4381|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4381A>T|||||4381|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3463A>T|||||3463|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3463A>T|||||3463|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2593A>T|||||2593|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2593A>T|||||2593|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2344A>T|||||2344|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2344A>T|||||2344|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1750A>T|||||1750|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1750A>T|||||1750|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1411A>T|||||1411|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1411A>T|||||1411|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*994A>T|||||994|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*994A>T|||||994|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*955A>T|||||955|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:50:48,2:48:1765:2:76:0,-7.83669,-151.894

+NC_045512.2	14442	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=7.35324;EPPR=90.593;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9691;PAIRED=1;PAIREDR=0.9375;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1805;RO=48;RPL=1;RPP=3.0103;RPPR=4.6389;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=25;SRP=3.19126;SRR=23;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14178T>C|p.Phe4726Phe|14178/21291|14178/21291|4726/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1002T>C|p.Phe334Phe|1002/2796|1002/2796|334/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1795T>C|||||1795|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3598T>C|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*959T>C|||||959|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4388T>C|||||4388|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4388T>C|||||4388|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3470T>C|||||3470|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3470T>C|||||3470|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2600T>C|||||2600|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2600T>C|||||2600|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2351T>C|||||2351|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2351T>C|||||2351|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1757T>C|||||1757|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1757T>C|||||1757|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1418T>C|||||1418|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1418T>C|||||1418|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1001T>C|||||1001|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1001T>C|||||1001|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*962T>C|||||962|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:50:48,2:48:1805:2:76:0,-7.83669,-155.498

+NC_045512.2	14450	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=5.18177;EPPR=19.0083;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=69.7847;PAIRED=1;PAIREDR=0.938776;PAO=0;PQA=0;PQR=0;PRO=0;QA=10;QR=1849;RO=49;RPL=1;RPP=5.18177;RPPR=45.5977;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=25;SRP=3.05462;SRR=24;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14186G>T|p.Gly4729Val|14186/21291|14186/21291|4729/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1010G>T|p.Gly337Val|1010/2796|1010/2796|337/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1787G>T|||||1787|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3590G>T|||||3590|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*967G>T|||||967|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4396G>T|||||4396|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4396G>T|||||4396|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3478G>T|||||3478|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3478G>T|||||3478|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2608G>T|||||2608|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2608G>T|||||2608|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2359G>T|||||2359|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2359G>T|||||2359|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1765G>T|||||1765|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1765G>T|||||1765|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1426G>T|||||1426|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1426G>T|||||1426|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1009G>T|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1009G>T|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*970G>T|||||970|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:50:49,1:49:1849:1:10:0,-14.0515,-165.672

+NC_045512.2	14531	.	C	A	3.80608E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=24;DPB=24;DPRA=0;EPP=5.18177;EPPR=52.9542;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=34.2448;PAIRED=1;PAIREDR=0.956522;PAO=0;PQA=0;PQR=0;PRO=0;QA=11;QR=872;RO=23;RPL=1;RPP=5.18177;RPPR=52.9542;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=0;SRP=52.9542;SRR=23;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14267C>A|p.Ser4756Tyr|14267/21291|14267/21291|4756/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1091C>A|p.Ser364Tyr|1091/2796|1091/2796|364/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1706C>A|||||1706|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3509C>A|||||3509|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1048C>A|||||1048|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4477C>A|||||4477|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4477C>A|||||4477|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3559C>A|||||3559|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3559C>A|||||3559|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2689C>A|||||2689|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2689C>A|||||2689|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2440C>A|||||2440|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2440C>A|||||2440|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1846C>A|||||1846|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1846C>A|||||1846|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1507C>A|||||1507|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1507C>A|||||1507|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1090C>A|||||1090|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1090C>A|||||1090|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1051C>A|||||1051|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:24:23,1:23:872:1:11:0,-6.12472,-77.7033

+NC_045512.2	14549	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=5.18177;EPPR=83.3548;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=52.9631;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=12;QR=1354;RO=37;RPL=0;RPP=5.18177;RPPR=10.1116;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=13;SRP=10.1116;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14285A>C|p.Glu4762Ala|14285/21291|14285/21291|4762/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1109A>C|p.Glu370Ala|1109/2796|1109/2796|370/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1688A>C|||||1688|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3491A>C|||||3491|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1066A>C|||||1066|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4495A>C|||||4495|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4495A>C|||||4495|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3577A>C|||||3577|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3577A>C|||||3577|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2707A>C|||||2707|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2707A>C|||||2707|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2458A>C|||||2458|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2458A>C|||||2458|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1864A>C|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1864A>C|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1525A>C|||||1525|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1525A>C|||||1525|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1108A>C|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1108A>C|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1069A>C|||||1069|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:38:37,1:37:1354:1:12:0,-10.2391,-120.954

+NC_045512.2	14550	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=39;DPB=39;DPRA=0;EPP=5.18177;EPPR=85.5263;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.87;PAIRED=1;PAIREDR=0.973684;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1385;RO=38;RPL=0;RPP=5.18177;RPPR=8.7247;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=14;SRP=8.7247;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14286A>C|p.Glu4762Asp|14286/21291|14286/21291|4762/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1110A>C|p.Glu370Asp|1110/2796|1110/2796|370/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1687A>C|||||1687|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3490A>C|||||3490|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1067A>C|||||1067|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4496A>C|||||4496|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4496A>C|||||4496|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3578A>C|||||3578|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3578A>C|||||3578|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2708A>C|||||2708|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2708A>C|||||2708|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2459A>C|||||2459|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2459A>C|||||2459|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1865A>C|||||1865|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1865A>C|||||1865|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1526A>C|||||1526|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1526A>C|||||1526|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1109A>C|||||1109|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1109A>C|||||1109|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1070A>C|||||1070|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:39:38,1:38:1385:1:27:0,-9.04039,-122.243

+NC_045512.2	14553	.	A	C	1.30189E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=98.5551;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=59.0447;PAIRED=1;PAIREDR=0.977273;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1634;RO=44;RPL=0;RPP=5.18177;RPPR=3.79993;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=20;SRP=3.79993;SRR=24;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14289A>C|p.Leu4763Phe|14289/21291|14289/21291|4763/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1113A>C|p.Leu371Phe|1113/2796|1113/2796|371/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1684A>C|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3487A>C|||||3487|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1070A>C|||||1070|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4499A>C|||||4499|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4499A>C|||||4499|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3581A>C|||||3581|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3581A>C|||||3581|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2711A>C|||||2711|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2711A>C|||||2711|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2462A>C|||||2462|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2462A>C|||||2462|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1868A>C|||||1868|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1868A>C|||||1868|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1529A>C|||||1529|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1529A>C|||||1529|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1112A>C|||||1112|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1112A>C|||||1112|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1073A>C|||||1073|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1634:1:27:0,-10.8466,-144.637

+NC_045512.2	14594	.	GTA	GA	8.14122E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D1M;DP=40;DPB=39.6667;DPRA=0;EPP=5.18177;EPPR=87.6977;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.6212;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=34;QR=1445;RO=39;RPL=1;RPP=5.18177;RPPR=4.40227;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=4.40227;SRR=17;TYPE=del;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14331delT|p.Asn4778fs|14331/21291|14331/21291|4777/7096||,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1155delT|p.Asn386fs|1155/2796|1155/2796|385/931||WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1642delT|||||1642|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3445delT|||||3445|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1112delT|||||1112|,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4541delT|||||4541|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4541delT|||||4541|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3623delT|||||3623|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3623delT|||||3623|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2753delT|||||2753|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2753delT|||||2753|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2504delT|||||2504|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2504delT|||||2504|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1910delT|||||1910|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1910delT|||||1910|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1571delT|||||1571|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1571delT|||||1571|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1154delT|||||1154|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1154delT|||||1154|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1115delT|||||1115|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1445:1:34:0,-8.64229,-126.939

+NC_045512.2	14598	.	T	G	1.37871E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=5.18177;EPPR=79.0118;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.8709;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=31;QR=1275;RO=35;RPL=1;RPP=5.18177;RPPR=8.03571;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=22;SRP=8.03571;SRR=13;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14334T>G|p.Asn4778Lys|14334/21291|14334/21291|4778/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1158T>G|p.Asn386Lys|1158/2796|1158/2796|386/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1639T>G|||||1639|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3442T>G|||||3442|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1115T>G|||||1115|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4544T>G|||||4544|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4544T>G|||||4544|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3626T>G|||||3626|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3626T>G|||||3626|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2756T>G|||||2756|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2756T>G|||||2756|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2507T>G|||||2507|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2507T>G|||||2507|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1913T>G|||||1913|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1913T>G|||||1913|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1574T>G|||||1574|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1574T>G|||||1574|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1157T>G|||||1157|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1157T>G|||||1157|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1118T>G|||||1118|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:36:35,1:35:1275:1:31:0,-7.73763,-111.948

+NC_045512.2	14667	.	T	G	1.65791E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=3.0103;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.2506;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1615;RO=43;RPL=0;RPP=7.35324;RPPR=96.3836;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14403T>G|p.Thr4801Thr|14403/21291|14403/21291|4801/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1227T>G|p.Thr409Thr|1227/2796|1227/2796|409/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1570T>G|||||1570|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3373T>G|||||3373|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4954T>G|||||4954|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1184T>G|||||1184|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4613T>G|||||4613|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4613T>G|||||4613|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3695T>G|||||3695|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3695T>G|||||3695|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2825T>G|||||2825|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2825T>G|||||2825|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2576T>G|||||2576|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2576T>G|||||2576|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1982T>G|||||1982|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1982T>G|||||1982|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1643T>G|||||1643|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1643T>G|||||1643|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1226T>G|||||1226|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1226T>G|||||1226|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1187T>G|||||1187|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:43,2:43:1615:2:76:0,-6.33154,-138.413

+NC_045512.2	14672	.	AACCC	GACCT,AACCT	443.765	.	AB=0.0444444,0.444444;ABP=84.1269,4.21667;AC=0,1;AF=0,0.5;AN=2;AO=2,20;CIGAR=1X3M1X,4M1X;DP=45;DPB=45;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.10471;GTI=0;LEN=5,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=102.181;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=76,754;QR=858;RO=23;RPL=0,0;RPP=7.35324,46.4397;RPPR=52.9542;RPR=2,20;RUN=1,1;SAF=1,10;SAP=3.0103,3.0103;SAR=1,10;SRF=11;SRP=3.10471;SRR=12;TYPE=complex,snp;ANN=GACCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14408_14412delAACCCinsGACCT|p.Lys4803Arg|14408/21291|14408/21291|4803/7096||,GACCT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1232_1236delAACCCinsGACCT|p.Lys411Arg|1232/2796|1232/2796|411/931||WARNING_TRANSCRIPT_NO_START_CODON,AACCT|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14412C>T|p.Pro4804Pro|14412/21291|14412/21291|4804/7096||,AACCT|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1236C>T|p.Pro412Pro|1236/2796|1236/2796|412/931||WARNING_TRANSCRIPT_NO_START_CODON,GACCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1565_-1561delAACCCinsGACCT|||||1565|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1561C>T|||||1561|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3368_-3364delAACCCinsGACCT|||||3368|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3364C>T|||||3364|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4949_-4945delAACCCinsGACCT|||||4949|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4945C>T|||||4945|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1189_*1193delAACCCinsGACCT|||||1189|,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1193C>T|||||1193|,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4618_*4622delAACCCinsGACCT|||||4618|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4622C>T|||||4622|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4618_*4622delAACCCinsGACCT|||||4618|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4622C>T|||||4622|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3700_*3704delAACCCinsGACCT|||||3700|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3704C>T|||||3704|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3700_*3704delAACCCinsGACCT|||||3700|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3704C>T|||||3704|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2830_*2834delAACCCinsGACCT|||||2830|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2834C>T|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2830_*2834delAACCCinsGACCT|||||2830|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2834C>T|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2581_*2585delAACCCinsGACCT|||||2581|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2585C>T|||||2585|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2581_*2585delAACCCinsGACCT|||||2581|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2585C>T|||||2585|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1987_*1991delAACCCinsGACCT|||||1987|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1991C>T|||||1991|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1987_*1991delAACCCinsGACCT|||||1987|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1991C>T|||||1991|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1648_*1652delAACCCinsGACCT|||||1648|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1652C>T|||||1652|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1648_*1652delAACCCinsGACCT|||||1648|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1652C>T|||||1652|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1231_*1235delAACCCinsGACCT|||||1231|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1235C>T|||||1235|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1231_*1235delAACCCinsGACCT|||||1231|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1235C>T|||||1235|WARNING_TRANSCRIPT_NO_START_CODON,GACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1192_*1196delAACCCinsGACCT|||||1192|WARNING_TRANSCRIPT_NO_START_CODON,AACCT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1196C>T|||||1196|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/2:45:23,2,20:23:858:2,20:76,754:-54.8669,-55.5573,-125.2,0,-64.0069,-64.2199

+NC_045512.2	14694	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=5.18177;EPPR=3.20771;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=58.3544;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1654;RO=44;RPL=0;RPP=5.18177;RPPR=98.5551;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=21;SRP=3.20771;SRR=23;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14430C>T|p.Asp4810Asp|14430/21291|14430/21291|4810/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1254C>T|p.Asp418Asp|1254/2796|1254/2796|418/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1543C>T|||||1543|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3346C>T|||||3346|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4927C>T|||||4927|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1211C>T|||||1211|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4640C>T|||||4640|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4640C>T|||||4640|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3722C>T|||||3722|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3722C>T|||||3722|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2852C>T|||||2852|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2852C>T|||||2852|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2603C>T|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2603C>T|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2009C>T|||||2009|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2009C>T|||||2009|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1670C>T|||||1670|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1670C>T|||||1670|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1253C>T|||||1253|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1253C>T|||||1253|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1214C>T|||||1214|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:44,1:44:1654:1:30:0,-10.5468,-146.133

+NC_045512.2	14708	.	C	A	1.65791E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=7.35324;EPPR=96.3836;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.2506;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1631;RO=43;RPL=1;RPP=3.0103;RPPR=3.0608;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14444C>A|p.Ala4815Asp|14444/21291|14444/21291|4815/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1268C>A|p.Ala423Asp|1268/2796|1268/2796|423/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1529C>A|||||1529|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3332C>A|||||3332|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4913C>A|||||4913|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1225C>A|||||1225|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4654C>A|||||4654|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4654C>A|||||4654|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3736C>A|||||3736|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3736C>A|||||3736|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2866C>A|||||2866|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2866C>A|||||2866|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2617C>A|||||2617|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2617C>A|||||2617|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2023C>A|||||2023|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2023C>A|||||2023|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1684C>A|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1684C>A|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1267C>A|||||1267|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1267C>A|||||1267|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1228C>A|||||1228|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:43,2:43:1631:2:76:0,-6.33154,-139.85

+NC_045512.2	14794	.	G	A	1.65791E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=3.0103;EPPR=3.0608;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=46.2506;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=1619;RO=43;RPL=2;RPP=7.35324;RPPR=96.3836;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=3.0608;SRR=22;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14530G>A|p.Asp4844Asn|14530/21291|14530/21291|4844/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1354G>A|p.Asp452Asn|1354/2796|1354/2796|452/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1443G>A|||||1443|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3246G>A|||||3246|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4827G>A|||||4827|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1311G>A|||||1311|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4740G>A|||||4740|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4740G>A|||||4740|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3822G>A|||||3822|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3822G>A|||||3822|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2952G>A|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2952G>A|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2703G>A|||||2703|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2703G>A|||||2703|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2109G>A|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2109G>A|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1770G>A|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1770G>A|||||1770|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1353G>A|||||1353|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1353G>A|||||1353|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1314G>A|||||1314|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:45:43,2:43:1619:2:76:0,-6.33154,-138.77

+NC_045512.2	14902	.	ATTAA	ATAA	1.31392E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1M1D3M;DP=40;DPB=39.8;DPRA=0;EPP=5.18177;EPPR=79.2345;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=49.704;PAIRED=1;PAIREDR=0.974359;PAO=0;PQA=0;PQR=0;PRO=0;QA=38;QR=1474;RO=39;RPL=1;RPP=5.18177;RPPR=4.40227;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=5.73856;SRR=23;TYPE=del;ANN=ATAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14640delT|p.Asn4881fs|14640/21291|14640/21291|4880/7096||,ATAA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1464delT|p.Asn489fs|1464/2796|1464/2796|488/931||WARNING_TRANSCRIPT_NO_START_CODON,ATAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1333delT|||||1333|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3136delT|||||3136|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4717delT|||||4717|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1421delT|||||1421|,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4850delT|||||4850|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4850delT|||||4850|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3932delT|||||3932|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3932delT|||||3932|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3062delT|||||3062|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3062delT|||||3062|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2813delT|||||2813|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2813delT|||||2813|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2219delT|||||2219|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2219delT|||||2219|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1880delT|||||1880|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1880delT|||||1880|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1463delT|||||1463|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1463delT|||||1463|WARNING_TRANSCRIPT_NO_START_CODON,ATAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1424delT|||||1424|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:40:39,1:39:1474:1:38:0,-8.24393,-129.148

+NC_045512.2	14924	.	T	G	1.49624E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=32;DPB=32;DPRA=0;EPP=5.18177;EPPR=61.9202;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.3638;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=1110;RO=31;RPL=1;RPP=5.18177;RPPR=3.64073;RPR=0;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14660T>G|p.Val4887Gly|14660/21291|14660/21291|4887/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1484T>G|p.Val495Gly|1484/2796|1484/2796|495/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1313T>G|||||1313|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3116T>G|||||3116|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4697T>G|||||4697|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1441T>G|||||1441|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4870T>G|||||4870|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4870T>G|||||4870|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3952T>G|||||3952|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3952T>G|||||3952|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3082T>G|||||3082|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3082T>G|||||3082|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2833T>G|||||2833|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2833T>G|||||2833|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2239T>G|||||2239|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2239T>G|||||2239|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1900T>G|||||1900|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1900T>G|||||1900|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1483T>G|||||1483|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1483T>G|||||1483|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1444T>G|||||1444|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:32:31,1:31:1110:1:27:0,-6.93318,-97.5053

+NC_045512.2	14978	.	G	T	3.63991E-12	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=31;DPB=31;DPRA=0;EPP=3.0103;EPPR=3.08518;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=27.8156;PAIRED=1;PAIREDR=0.965517;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=1087;RO=29;RPL=0;RPP=7.35324;RPPR=65.983;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=15;SRP=3.08518;SRR=14;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14714G>T|p.Arg4905Ile|14714/21291|14714/21291|4905/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1538G>T|p.Arg513Ile|1538/2796|1538/2796|513/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1259G>T|||||1259|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3062G>T|||||3062|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4643G>T|||||4643|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1495G>T|||||1495|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4924G>T|||||4924|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4924G>T|||||4924|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4006G>T|||||4006|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4006G>T|||||4006|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3136G>T|||||3136|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3136G>T|||||3136|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2887G>T|||||2887|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2887G>T|||||2887|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2293G>T|||||2293|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2293G>T|||||2293|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1954G>T|||||1954|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1954G>T|||||1954|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1537G>T|||||1537|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1537G>T|||||1537|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1498G>T|||||1498|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:31:29,2:29:1087:2:75:0,-2.21159,-91.0197