Mercurial > repos > iuc > snpeff_sars_cov_2
changeset 0:2a3a00c1fa0a draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e6d1b32be9df14beb1e2859a0d2fa29a2d09227e"
| author | iuc |
|---|---|
| date | Thu, 18 Jun 2020 16:11:49 -0400 |
| parents | |
| children | |
| files | snpEff.xml snpEff_macros.xml test-data/input.vcf test-data/output.vcf |
| diffstat | 4 files changed, 625 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff.xml Thu Jun 18 16:11:49 2020 -0400 @@ -0,0 +1,363 @@ +<tool id="snpeff_sars_cov_2" name="SnpEff eff:" version="@WRAPPER_VERSION@"> + <description> annotate variants for SARS-CoV-2</description> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <requirements> + <expand macro="requirement" /> + </requirements> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + snpEff @JAVA_OPTIONS@ eff + -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength + #if $annotations and str($annotations) != '': + #echo " " + #echo ' '.join(str($annotations).split(',')) + #end if + #if $filterOut and str($filterOut) != '': + #echo " " + #echo ' '.join(str($filterOut).split(',')) + #end if + #if $filter.specificEffects == 'yes' and $filter.effects: + #for $eff in str($filter.effects).split(','): + -no $eff + #end for + #end if + #if $transcripts + -onlyTr '$transcripts' + #end if + #if $intervals ### fix this for multiple dataset input + -interval '$intervals' + #end if + #if $statsFile: + -stats '$statsFile' + #end if + #if $csvStats: + -csvStats '$csvFile' + #end if + #if str($offset) != 'default': + ${offset} + #end if + #if str($chr).strip() != '': + -chr '$chr' + #end if + $noLog + + $genome_version + + '$input' > '$snpeff_output' + + #if $statsFile: + && + #import os + #if $csvStats: + #set $genes_file = str($csvFile) + '.genes.txt' + #else + #set $genes_file = str($statsFile) + '.genes.txt' + #end if + #set $genes_file_name = os.path.split($genes_file)[-1] + mkdir '$statsFile.files_path' && + mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#' + #end if + #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 + && + ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" + sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output' + #end if + ]]></command> + <inputs> + <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/> + + <param name="inputFormat" type="select" label="Input format"> + <option value="vcf" selected="true">VCF</option> + <option value="bed">BED (Deprecated)</option> + </param> + + <param name="genome_version" type="select" label="Select an annotated Coronavirus genome"> + <option value="NC_045512.2">NC_045512.2: COVID19 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1</option> + <option value="DQ648856.1">DQ648856.1: Bat coronavirus (BtCoV/273/2005), complete genome.</option> + <option value="DQ648857.1">DQ648857.1: Bat coronavirus (BtCoV/279/2005), complete genome.</option> + <option value="JX993988.1">JX993988.1: Bat coronavirus Cp/Yunnan2011, complete genome.</option> + <option value="MN996532.1">MN996532.1: Bat coronavirus RaTG13, complete genome.</option> + <option value="JX993987.1">JX993987.1: Bat coronavirus Rp/Shaanxi2011, complete genome.</option> + <option value="GQ153545.1">GQ153545.1: Bat SARS coronavirus HKU3-10, complete genome.</option> + <option value="GQ153546.1">GQ153546.1: Bat SARS coronavirus HKU3-11, complete genome.</option> + <option value="GQ153547.1">GQ153547.1: Bat SARS coronavirus HKU3-12, complete genome.</option> + <option value="DQ022305.2">DQ022305.2: Bat SARS coronavirus HKU3-1, complete genome.</option> + <option value="DQ084199.1">DQ084199.1: bat SARS coronavirus HKU3-2, complete genome.</option> + <option value="DQ084200.1">DQ084200.1: bat SARS coronavirus HKU3-3, complete genome.</option> + <option value="GQ153539.1">GQ153539.1: Bat SARS coronavirus HKU3-4, complete genome.</option> + <option value="GQ153540.1">GQ153540.1: Bat SARS coronavirus HKU3-5, complete genome.</option> + <option value="GQ153541.1">GQ153541.1: Bat SARS coronavirus HKU3-6, complete genome.</option> + <option value="GQ153542.1">GQ153542.1: Bat SARS coronavirus HKU3-7, complete genome.</option> + <option value="GQ153543.1">GQ153543.1: Bat SARS coronavirus HKU3-8, complete genome.</option> + <option value="GQ153544.1">GQ153544.1: Bat SARS coronavirus HKU3-9, complete genome.</option> + <option value="FJ588686.1">FJ588686.1: Bat SARS CoV Rs672/2006, complete genome.</option> + <option value="KC881006.1">KC881006.1: Bat SARS-like coronavirus Rs3367, complete genome.</option> + <option value="KC881005.1">KC881005.1: Bat SARS-like coronavirus RsSHC014, complete genome.</option> + <option value="KF367457.1">KF367457.1: Bat SARS-like coronavirus WIV1, complete genome.</option> + <option value="KP886808.1">KP886808.1: Bat SARS-like coronavirus YNLF_31C, complete genome.</option> + <option value="KP886809.1">KP886809.1: Bat SARS-like coronavirus YNLF_34C, complete genome.</option> + <option value="KJ473812.1">KJ473812.1: BtRf-BetaCoV/HeB2013, complete genome.</option> + <option value="KJ473811.1">KJ473811.1: BtRf-BetaCoV/JL2012, complete genome.</option> + <option value="KJ473813.1">KJ473813.1: BtRf-BetaCoV/SX2013, complete genome.</option> + <option value="KJ473815.1">KJ473815.1: BtRs-BetaCoV/GX2013, complete genome.</option> + <option value="KJ473814.1">KJ473814.1: BtRs-BetaCoV/HuB2013, complete genome.</option> + <option value="KJ473816.1">KJ473816.1: BtRs-BetaCoV/YN2013, complete genome.</option> + <option value="KF569996.1">KF569996.1: Rhinolophus affinis coronavirus isolate LYRa11, complete genome.</option> + <option value="AY687354.1">AY687354.1: SARS coronavirus A001 spike glycoprotein gene, complete cds.</option> + <option value="AY687355.1">AY687355.1: SARS coronavirus A013 spike glycoprotein gene, complete cds.</option> + <option value="AY687356.1">AY687356.1: SARS coronavirus A021 spike glycoprotein gene, complete cds.</option> + <option value="AY686863.1">AY686863.1: SARS coronavirus A022, complete genome.</option> + <option value="AY687357.1">AY687357.1: SARS coronavirus A030 spike glycoprotein gene, complete cds.</option> + <option value="AY687358.1">AY687358.1: SARS coronavirus A031 spike glycoprotein gene, complete cds.</option> + <option value="AY427439.1">AY427439.1: SARS coronavirus AS, complete genome.</option> + <option value="AY687359.1">AY687359.1: SARS coronavirus B012 spike glycoprotein gene, complete cds.</option> + <option value="AY687360.1">AY687360.1: SARS coronavirus B024 spike glycoprotein gene, complete cds.</option> + <option value="AY687361.1">AY687361.1: SARS coronavirus B029 spike glycoprotein gene, complete cds.</option> + <option value="AY687362.1">AY687362.1: SARS coronavirus B033 spike glycoprotein gene, complete cds.</option> + <option value="AY686864.1">AY686864.1: SARS coronavirus B039, complete genome.</option> + <option value="AY687364.1">AY687364.1: SARS coronavirus B040 spike glycoprotein gene, complete cds.</option> + <option value="AY278488.2">AY278488.2: SARS coronavirus BJ01, complete genome.</option> + <option value="AY279354.2">AY279354.2: SARS coronavirus BJ04, complete genome.</option> + <option value="AY864805.1">AY864805.1: SARS coronavirus BJ162, complete genome.</option> + <option value="EU371564.1">EU371564.1: SARS coronavirus BJ182-12, complete genome.</option> + <option value="EU371562.1">EU371562.1: SARS coronavirus BJ182-4, complete genome.</option> + <option value="EU371563.1">EU371563.1: SARS coronavirus BJ182-8, complete genome.</option> + <option value="EU371560.1">EU371560.1: SARS coronavirus BJ182a, complete genome.</option> + <option value="EU371561.1">EU371561.1: SARS coronavirus BJ182b, complete genome.</option> + <option value="AY864806.1">AY864806.1: SARS coronavirus BJ202, complete genome.</option> + <option value="AY340092.1">AY340092.1: SARS coronavirus BJ2232 RNA polymerase gene, partial cds.</option> + <option value="AY714217.1">AY714217.1: SARS Coronavirus CDC#200301157, complete genome.</option> + <option value="AY572034.1">AY572034.1: SARS coronavirus civet007, complete genome.</option> + <option value="AY572035.1">AY572035.1: SARS coronavirus civet010, complete genome.</option> + <option value="AY572038.1">AY572038.1: SARS coronavirus civet020, complete genome.</option> + <option value="AY345986.1">AY345986.1: SARS coronavirus CUHK-AG01, complete genome.</option> + <option value="AY345987.1">AY345987.1: SARS coronavirus CUHK-AG02, complete genome.</option> + <option value="AY345988.1">AY345988.1: SARS coronavirus CUHK-AG03, complete genome.</option> + <option value="AY282752.2">AY282752.2: SARS coronavirus CUHK-Su10, complete genome.</option> + <option value="AY278554.2">AY278554.2: SARS coronavirus CUHK-W1, complete genome.</option> + <option value="AY310120.1">AY310120.1: SARS coronavirus FRA, complete genome.</option> + <option value="AY278489.2">AY278489.2: SARS coronavirus GD01, complete genome.</option> + <option value="AY313906.1">AY313906.1: SARS coronavirus GD69, complete genome.</option> + <option value="DQ640652.1">DQ640652.1: SARS coronavirus GDH-BJH01, complete genome.</option> + <option value="AY390556.1">AY390556.1: SARS coronavirus GZ02, complete genome.</option> + <option value="AY568539.1">AY568539.1: SARS coronavirus GZ0401, complete genome.</option> + <option value="AY613947.1">AY613947.1: SARS coronavirus GZ0402, complete genome.</option> + <option value="AY304495.1">AY304495.1: SARS coronavirus GZ50, complete genome.</option> + <option value="AY394978.1">AY394978.1: SARS coronavirus GZ-B, complete genome.</option> + <option value="AY394979.1">AY394979.1: SARS coronavirus GZ-C, complete genome.</option> + <option value="AY515512.1">AY515512.1: SARS coronavirus HC/SZ/61/03, complete genome.</option> + <option value="JQ316196.1">JQ316196.1: SARS coronavirus HKU-39849 isolate UOB, complete genome.</option> + <option value="AY323977.2">AY323977.2: SARS coronavirus HSR 1, complete genome.</option> + <option value="AY595412.1">AY595412.1: SARS coronavirus LLJ-2004, complete genome.</option> + <option value="AY508724.1">AY508724.1: SARS coronavirus NS-1, complete genome.</option> + <option value="FJ882963.1">FJ882963.1: SARS coronavirus P2, complete genome.</option> + <option value="AY350750.1">AY350750.1: SARS coronavirus PUMC01, complete genome.</option> + <option value="AY357075.1">AY357075.1: SARS coronavirus PUMC02, complete genome.</option> + <option value="AY357076.1">AY357076.1: SARS coronavirus PUMC03, complete genome.</option> + <option value="AY463059.1">AY463059.1: SARS coronavirus ShanghaiQXC1, complete genome.</option> + <option value="AY463060.1">AY463060.1: SARS coronavirus ShanghaiQXC2, complete genome.</option> + <option value="AY485277.1">AY485277.1: SARS coronavirus Sino1-11, complete genome.</option> + <option value="AY485278.1">AY485278.1: SARS coronavirus Sino3-11, complete genome.</option> + <option value="AY304488.1">AY304488.1: SARS coronavirus SZ16, complete genome.</option> + <option value="AY304486.1">AY304486.1: SARS coronavirus SZ3, complete genome.</option> + <option value="AY338174.1">AY338174.1: SARS coronavirus Taiwan TC1, complete genome.</option> + <option value="AY338175.1">AY338175.1: SARS coronavirus Taiwan TC2, complete genome.</option> + <option value="AY348314.1">AY348314.1: SARS coronavirus Taiwan TC3, complete genome.</option> + <option value="AY654624.1">AY654624.1: SARS coronavirus TJF, complete genome.</option> + <option value="AY502923.1">AY502923.1: SARS coronavirus TW10, complete genome.</option> + <option value="AY502924.1">AY502924.1: SARS coronavirus TW11, complete genome.</option> + <option value="AY291451.1">AY291451.1: SARS coronavirus TW1, complete genome.</option> + <option value="AY502925.1">AY502925.1: SARS coronavirus TW2, complete genome.</option> + <option value="AY502926.1">AY502926.1: SARS coronavirus TW3, complete genome.</option> + <option value="AY502927.1">AY502927.1: SARS coronavirus TW4, complete genome.</option> + <option value="AY502928.1">AY502928.1: SARS coronavirus TW5, complete genome.</option> + <option value="AY502929.1">AY502929.1: SARS coronavirus TW6, complete genome.</option> + <option value="AY502930.1">AY502930.1: SARS coronavirus TW7, complete genome.</option> + <option value="AY502931.1">AY502931.1: SARS coronavirus TW8, complete genome.</option> + <option value="AY502932.1">AY502932.1: SARS coronavirus TW9, complete genome.</option> + <option value="AP006557.1">AP006557.1: SARS coronavirus TWH genomic RNA, complete genome.</option> + <option value="AP006558.1">AP006558.1: SARS coronavirus TWJ genomic RNA, complete genome.</option> + <option value="AP006559.1">AP006559.1: SARS coronavirus TWK genomic RNA, complete genome.</option> + <option value="AP006560.1">AP006560.1: SARS coronavirus TWS genomic RNA, complete genome.</option> + <option value="AP006561.1">AP006561.1: SARS coronavirus TWY genomic RNA, complete genome.</option> + <option value="AY278741.1">AY278741.1: SARS coronavirus Urbani, complete genome.</option> + <option value="MK062181.1">MK062181.1: SARS coronavirus Urbani isolate icSARS-C3, complete genome.</option> + <option value="MK062182.1">MK062182.1: SARS coronavirus Urbani isolate icSARS-C3-MA, complete genome.</option> + <option value="MK062183.1">MK062183.1: SARS coronavirus Urbani isolate icSARS-C7, complete genome.</option> + <option value="MK062184.1">MK062184.1: SARS coronavirus Urbani isolate icSARS-C7-MA, complete genome.</option> + <option value="MK062179.1">MK062179.1: SARS coronavirus Urbani isolate icSARS, complete genome.</option> + <option value="MK062180.1">MK062180.1: SARS coronavirus Urbani isolate icSARS-MA, complete genome.</option> + <option value="AY772062.1">AY772062.1: SARS coronavirus WH20, complete genome.</option> + <option value="EU371559.1">EU371559.1: SARS coronavirus ZJ02, complete genome.</option> + <option value="DQ182595.1">DQ182595.1: SARS coronavirus ZJ0301 from China, complete genome.</option> + </param> + + <conditional name="outputConditional"> + <param name="outputFormat" type="select" label="Output format"> + <option value="vcf" selected="true">VCF (only if input is VCF)</option> + <option value="gatk">GATK-compatible VCF (only if input is VCF)</option> + <option value="bed">BED</option> + <option value="bedAnn">BED annotations</option> + </param> + <when value="vcf" /> + <when value="gatk"> + <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" /> + </when> + <when value="bed" /> + <when value="bedAnn" /> + </conditional> + <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" /> + + <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length"> + <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option> + <option value="10">10 bases</option> + <option value="50">50 bases</option> + <option value="100">100 bases</option> + <option value="200">200 bases</option> + <option value="500">500 bases</option> + <option value="1000">1000 bases</option> + <option value="2000">2000 bases</option> + <option value="5000">5000 bases</option> + </param> + + <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> + <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option> + <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option> + <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> + <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> + <option value="-hgvsOld">Old notation style notation: E.g. 'c.G123T' instead of 'c.123G>T' and 'X' instead of '*'</option> + <option value="-hgvs1LetterAa">Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly</option> + <option value="-hgvsTrId">Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G</option> + <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end)</option> + <option value="-noHgvs">Do not add HGVS annotations</option> + <option value="-canon">Only use canonical transcripts</option> + <option value="-onlyProtein">Only use protein coding transcripts</option> + <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> + <option value="-noExpandIUB">Disable IUB code expansion in input variants</option> + <option value="-oicr">Add OICR tag in VCF file</option> + <option value="-noLof">Do not add LOF and NMD annotations</option> + <option value="-noInteraction">Disable interaction annotations</option> + </param> + <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. --> + <param name="intervals" argument="-interval" type="data" format="bed" optional="true" label="Use custom interval file for annotation" /> + <param name="transcripts" type="data" format="tabular" optional="true" label="Only use the transcripts in this file" help="Format is one transcript ID per line"/> + <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> + <option value="-no-downstream">Do not show DOWNSTREAM changes</option> + <option value="-no-intergenic">Do not show INTERGENIC changes</option> + <option value="-no-upstream">Do not show UPSTREAM changes</option> + <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option> + </param> + <conditional name="filter"> + <param name="specificEffects" type="select" label="Filter out specific Effects"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects"> + <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option> + <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option> + <option value="CODON_CHANGE">CODON_CHANGE (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3 MODERATE</option> + <option value="CODON_INSERTION">CODON_INSERTION (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary MODERATE</option> + <option value="CODON_CHANGE_PLUS_CODON_INSERTION">CODON_CHANGE_PLUS_CODON_INSERTION (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary MODERATE</option> + <option value="CODON_DELETION">CODON_DELETION (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary MODERATE</option> + <option value="CODON_CHANGE_PLUS_CODON_DELETION">CODON_CHANGE_PLUS_CODON_DELETION (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary MODERATE</option> + <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option> + <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option> + <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option> + <option value="FRAME_SHIFT">FRAME_SHIFT (frameshift_variant) Insertion or deletion causes a frame shift e.g.: An indel size is not multple of 3 HIGH</option> + <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option> + <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option> + <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option> + <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option> + <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option> + <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option> + <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option> + <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING (missense_variant) Variant causes a codon that produces a different amino acid e.g.: Tgg/Cgg, W/R MODERATE</option> + <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START (initiator_codon_variant) Variant causes start codon to be mutated into another start codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option> + <option value="NON_SYNONYMOUS_STOP">NON_SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option> + <option value="RARE_AMINO_ACID">RARE_AMINO_ACID (rare_amino_acid_variant) The variant hits a rare amino acid thus is likely to produce protein loss of function HIGH</option> + <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR (splice_acceptor_variant) The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon). HIGH</option> + <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR (splice_donor_variant) The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon). HIGH</option> + <option value="SPLICE_SITE_REGION">SPLICE_SITE_REGION (splice_region_variant) A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. LOW</option> + <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option> + <option value="SPLICE_SITE_BRANCH_U12">SPLICE_SITE_BRANCH_U12 (splice_region_variant) A varaint affective putative (Lariat) branch point from U12 splicing machinery, located in the intron. MODERATE</option> + <option value="STOP_LOST">STOP_LOST (stop_lost) Variant causes stop codon to be mutated into a non-stop codon e.g.: Tga/Cga, */R HIGH</option> + <option value="START_GAINED">START_GAINED (5_prime_UTR_premature start_codon_gain_variant) A variant in 5'UTR region produces a three base sequence that can be a START codon. LOW</option> + <option value="START_LOST">START_LOST (start_lost) Variant causes start codon to be mutated into a non-start codon. e.g.: aTg/aGg, M/R HIGH</option> + <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option> + <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING (synonymous_variant) Variant causes a codon that produces the same amino acid e.g.: Ttg/Ctg, L/L LOW</option> + <option value="SYNONYMOUS_START">SYNONYMOUS_START (start_retained) Variant causes start codon to be mutated into another start codon. e.g.: Ttg/Ctg, L/L (TTG and CTG can be START codons) LOW</option> + <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon. e.g.: taA/taG, */* LOW</option> + <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option> + <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option> + <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option> + <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option> + <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3'UTR of the transcript MODERATE</option> + <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option> + <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option> + </param> + </when> + </conditional> + + <param name="offset" type="select" display="radio" label="Chromosomal position"> + <option value="default" selected="true">Use default (based on input type)</option> + <option value="-0">Force zero-based positions (both input and output)</option> + <option value="-1">Force one-based positions (both input and output)</option> + </param> + <param argument="-chr" type="text" label="Text to prepend to chromosome name"> + <help> + By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. + You can prepend any string you want to the chromosome name + </help> + <validator type="regex" message="No whitespace allowed">^\S*$</validator> + </param> + <param name="generate_stats" argument="-noStats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats" /> + <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" /> + </inputs> + <outputs> + <data name="snpeff_output" format="vcf"> + <change_format> + <when input="outputConditional.outputFormat" value="bed" format="bed" /> + <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> + </change_format> + </data> + <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats"> + <filter>generate_stats == True</filter> + </data> + <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats"> + <filter>csvStats == True</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" ftype="vcf" value="input.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genome_version" value="NC_045512.2" /> + <param name="udLength" value="0"/> + <param name="generate_stats" value="false"/> + <output name="snpeff_output" file="output.vcf" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +**This is a special edition of SnpEff tweaked for SARS-CoV-2 variant annotation.** + +SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). + +A typical SnpEff use case would be: + + - **Input**: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF). + - **Output**: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). + +@SNPEFF_IN_GALAXY_INFO@ +@EXTERNAL_DOCUMENTATION@ +]]> + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_macros.xml Thu Jun 18 16:11:49 2020 -0400 @@ -0,0 +1,51 @@ +<macros> + <xml name="requirement"> + <requirement type="package" version="4.5covid19">snpeff</requirement> + <yield/> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <xml name="version_command"> + <version_command><![CDATA[ +snpEff -version + ]]></version_command> + </xml> + <token name="@WRAPPER_VERSION@">4.5covid19</token> + <token name="@SNPEFF_VERSION@">SnpEff4.5</token> + <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token> + <token name="@EXTERNAL_DOCUMENTATION@"> + + +------- + +To learn more about SnpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html + </token> + <token name="@SNPEFF_IN_GALAXY_INFO@"> + +------- + +.. class:: warningmark + +**Databases in the SnpEff Covid-19 edition** + +This special version of SnpEff provides only a fixed number of +SARS-CoV-2-related genome databases. + +Unlike with regular SnpEff releases, it is not possible to extend this set, +*i.e*, you cannot download additional databases or build custom databases for +this edition. +</token> + + + + <xml name="citations"> + <citations> + <citation type="doi">10.4161/fly.19695</citation> + <yield /> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.vcf Thu Jun 18 16:11:49 2020 -0400 @@ -0,0 +1,103 @@ +##fileformat=VCFv4.0 +##fileDate=20200606 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 50 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --def-alt-bq 0 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/008/613/8613450/working/pp-tmp/lofreq2_call_paralleltqdqbfki/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_62,Description="Minimum SNV Quality (Phred) 62"> +##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50"> +##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##FILTER=<ID=min_snvqual_65,Description="Minimum SNV Quality (Phred) 65"> +##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 105 . G T 3155.0 PASS DP=748;AF=0.171123;SB=0;DP4=600,20,124,4 +NC_045512.2 443 . GT G 99.0 PASS DP=1286;AF=0.004666;SB=0;DP4=718,586,3,3;INDEL;HRUN=4 +NC_045512.2 507 . ATGGTCATGTTATGGT A 100.0 PASS DP=1554;AF=0.003861;SB=10;DP4=684,865,5,1;INDEL;HRUN=1 +NC_045512.2 509 . GGTCATGTTATGGTT G 99.0 PASS DP=1567;AF=0.003829;SB=0;DP4=706,873,3,3;INDEL;HRUN=2 +NC_045512.2 514 . TGTTATG T 118.0 PASS DP=1696;AF=0.004127;SB=1;DP4=865,826,3,4;INDEL;HRUN=1 +NC_045512.2 515 . GTTATGGTT G 59.0 PASS DP=1706;AF=0.002345;SB=4;DP4=887,826,1,3;INDEL;HRUN=2 +NC_045512.2 517 . TATG T 91.0 PASS DP=1733;AF=0.003462;SB=15;DP4=882,856,6,0;INDEL;HRUN=1 +NC_045512.2 518 . ATG A 53.0 PASS DP=1679;AF=0.002382;SB=4;DP4=892,842,1,3;INDEL;HRUN=1 +NC_045512.2 518 . ATGGTT A 78.0 PASS DP=1679;AF=0.002978;SB=1;DP4=892,842,2,3;INDEL;HRUN=1 +NC_045512.2 685 . AAAGTCATTT A 60.0 PASS DP=1188;AF=0.003367;SB=2;DP4=607,618,1,3;INDEL;HRUN=3 +NC_045512.2 1011 . ATG A 77.0 PASS DP=1345;AF=0.003717;SB=1;DP4=927,454,3,2;INDEL;HRUN=1 +NC_045512.2 1135 . G GA 93.0 PASS DP=1272;AF=0.004717;SB=3;DP4=663,650,2,4;INDEL;HRUN=5 +NC_045512.2 1349 . C CA 257.0 PASS DP=1121;AF=0.011597;SB=1;DP4=444,668,6,7;INDEL;HRUN=4 +NC_045512.2 1730 . G A 116.0 PASS DP=997;AF=0.009027;SB=2;DP4=440,548,5,4 +NC_045512.2 1946 . G GT 206.0 PASS DP=1976;AF=0.006073;SB=0;DP4=982,986,6,6;INDEL;HRUN=4 +NC_045512.2 2185 . G GT 73.0 PASS DP=2095;AF=0.002387;SB=4;DP4=1374,803,2,3;INDEL;HRUN=3 +NC_045512.2 2310 . TA T 56.0 PASS DP=2134;AF=0.001874;SB=2;DP4=1056,1084,1,3;INDEL;HRUN=3 +NC_045512.2 2480 . A G 49314.0 PASS DP=2088;AF=0.986590;SB=3;DP4=1,0,890,1196 +NC_045512.2 2558 . C T 49314.0 PASS DP=2141;AF=0.983652;SB=0;DP4=0,1,736,1402 +NC_045512.2 2612 . G GT 58.0 PASS DP=1770;AF=0.002260;SB=4;DP4=884,972,3,1;INDEL;HRUN=3 +NC_045512.2 3259 . G T 69.0 PASS DP=1704;AF=0.004108;SB=25;DP4=723,974,7,0 +NC_045512.2 3412 . T TA 69.0 PASS DP=1670;AF=0.002994;SB=0;DP4=803,866,2,3;INDEL;HRUN=5 +NC_045512.2 3448 . C CA 59.0 PASS DP=1732;AF=0.002309;SB=0;DP4=733,997,2,2;INDEL;HRUN=2 +NC_045512.2 3545 . AATG A 57.0 PASS DP=2002;AF=0.001998;SB=4;DP4=945,1062,3,1;INDEL;HRUN=2 +NC_045512.2 4148 . G GT 63.0 PASS DP=1147;AF=0.003487;SB=1;DP4=474,683,1,3;INDEL;HRUN=4 +NC_045512.2 6287 . TG T 60.0 PASS DP=1537;AF=0.002602;SB=2;DP4=810,729,3,1;INDEL;HRUN=2 +NC_045512.2 6696 . C CT 1002.0 PASS DP=1985;AF=0.022670;SB=1;DP4=739,1238,18,27;INDEL;HRUN=4 +NC_045512.2 6696 . C T 141.0 PASS DP=2023;AF=0.006920;SB=0;DP4=752,1256,5,10 +NC_045512.2 7504 . C CA 57.0 PASS DP=1874;AF=0.002134;SB=0;DP4=990,903,2,2;INDEL;HRUN=3 +NC_045512.2 9118 . C T 170.0 PASS DP=2259;AF=0.006640;SB=14;DP4=1213,1031,4,11 +NC_045512.2 9502 . C T 221.0 PASS DP=2082;AF=0.009606;SB=0;DP4=836,1225,8,12 +NC_045512.2 9701 . AT A 59.0 PASS DP=1741;AF=0.002298;SB=2;DP4=843,930,1,3;INDEL;HRUN=3 +NC_045512.2 10605 . C CT 116.0 PASS DP=2586;AF=0.003094;SB=0;DP4=1507,1082,5,3;INDEL;HRUN=4 +NC_045512.2 10619 . C A 235.0 PASS DP=2564;AF=0.007800;SB=5;DP4=1272,1272,7,13 +NC_045512.2 10660 . TA T 122.0 PASS DP=2326;AF=0.003439;SB=15;DP4=1292,1057,1,7;INDEL;HRUN=2 +NC_045512.2 11074 . C CT 281.0 PASS DP=1459;AF=0.036326;SB=2;DP4=822,613,28,25;INDEL;HRUN=8 +NC_045512.2 11082 . TG T 1843.0 PASS DP=1309;AF=0.058060;SB=0;DP4=662,589,39,37;INDEL;HRUN=1 +NC_045512.2 11083 . G T 39536.0 PASS DP=1319;AF=0.918120;SB=0;DP4=0,0,645,595 +NC_045512.2 11133 . CT C 60.0 PASS DP=1181;AF=0.003387;SB=2;DP4=607,573,3,1;INDEL;HRUN=4 +NC_045512.2 11301 . TA T 104.0 PASS DP=2098;AF=0.003337;SB=9;DP4=796,1299,5,2;INDEL;HRUN=4 +NC_045512.2 11812 . C CA 215.0 PASS DP=2020;AF=0.005941;SB=0;DP4=891,1127,5,7;INDEL;HRUN=3 +NC_045512.2 11812 . C A 104.0 PASS DP=2030;AF=0.004926;SB=13;DP4=895,1123,1,9 +NC_045512.2 12296 . C CA 222.0 PASS DP=1709;AF=0.007022;SB=6;DP4=573,1131,6,6;INDEL;HRUN=3 +NC_045512.2 14110 . C CA 57.0 PASS DP=1940;AF=0.002062;SB=0;DP4=872,1128,2,2;INDEL;HRUN=3 +NC_045512.2 14205 . A C 790.0 PASS DP=2047;AF=0.023449;SB=38;DP4=1106,890,41,9 +NC_045512.2 14327 . C CA 59.0 PASS DP=1729;AF=0.002313;SB=0;DP4=693,1040,2,2;INDEL;HRUN=3 +NC_045512.2 14432 . G GA 118.0 PASS DP=1895;AF=0.004222;SB=3;DP4=1004,913,3,5;INDEL;HRUN=5 +NC_045512.2 14625 . C T 78.0 PASS DP=2695;AF=0.003340;SB=3;DP4=2134,550,7,3 +NC_045512.2 14745 . TGAATTA T 111.0 PASS DP=2063;AF=0.003393;SB=8;DP4=975,1086,1,6;INDEL;HRUN=1 +NC_045512.2 14805 . C T 49314.0 PASS DP=2660;AF=0.987594;SB=0;DP4=0,0,1259,1398 +NC_045512.2 14852 . TTGTA T 67.0 PASS DP=2763;AF=0.001810;SB=1;DP4=1578,1259,2,3;INDEL;HRUN=3 +NC_045512.2 17916 . AT A 53.0 PASS DP=2304;AF=0.001736;SB=4;DP4=1310,1011,1,3;INDEL;HRUN=3 +NC_045512.2 18350 . ATTTACC A 57.0 PASS DP=1950;AF=0.002051;SB=0;DP4=974,1048,2,2;INDEL;HRUN=3 +NC_045512.2 18688 . T C 93.0 PASS DP=1875;AF=0.005333;SB=9;DP4=938,925,8,2 +NC_045512.2 19017 . C T 86.0 PASS DP=2058;AF=0.004373;SB=1;DP4=910,1138,3,6 +NC_045512.2 19188 . A AT 55.0 PASS DP=1835;AF=0.002180;SB=5;DP4=769,1067,3,1;INDEL;HRUN=4 +NC_045512.2 19983 . C CT 137.0 PASS DP=1533;AF=0.007828;SB=0;DP4=652,888,5,7;INDEL;HRUN=6 +NC_045512.2 20091 . C CA 81.0 PASS DP=1477;AF=0.003385;SB=4;DP4=814,661,4,1;INDEL;HRUN=3 +NC_045512.2 20296 . AAATT A 64.0 PASS DP=1333;AF=0.003001;SB=2;DP4=423,909,2,2;INDEL;HRUN=3 +NC_045512.2 20890 . G GT 63.0 PASS DP=1405;AF=0.002847;SB=2;DP4=957,485,2,2;INDEL;HRUN=2 +NC_045512.2 21101 . G GT 105.0 PASS DP=1133;AF=0.007944;SB=1;DP4=525,606,5,4;INDEL;HRUN=6 +NC_045512.2 22383 . C CT 64.0 PASS DP=978;AF=0.004090;SB=4;DP4=454,598,3,1;INDEL;HRUN=4 +NC_045512.2 22583 . G GT 124.0 PASS DP=874;AF=0.008009;SB=0;DP4=472,402,4,3;INDEL;HRUN=5 +NC_045512.2 22802 . C CA 87.0 PASS DP=1083;AF=0.004617;SB=1;DP4=646,483,2,3;INDEL;HRUN=3 +NC_045512.2 23191 . C T 5808.0 PASS DP=1605;AF=0.149533;SB=8;DP4=895,464,150,96 +NC_045512.2 23568 . GTA G 66.0 PASS DP=2956;AF=0.001691;SB=1;DP4=1354,1607,3,2;INDEL;HRUN=1 +NC_045512.2 23621 . G A 76.0 PASS DP=2968;AF=0.003032;SB=1;DP4=1090,1868,4,5 +NC_045512.2 23735 . G GA 53.0 PASS DP=2490;AF=0.001606;SB=0;DP4=629,1866,1,3;INDEL;HRUN=3 +NC_045512.2 23835 . G GT 71.0 PASS DP=1518;AF=0.003294;SB=4;DP4=924,620,2,3;INDEL;HRUN=5 +NC_045512.2 24025 . ACTT A 76.0 PASS DP=1327;AF=0.003768;SB=4;DP4=523,808,3,2;INDEL;HRUN=1 +NC_045512.2 24358 . C CA 80.0 PASS DP=1275;AF=0.003922;SB=1;DP4=861,420,3,2;INDEL;HRUN=4 +NC_045512.2 24858 . G A 74.0 PASS DP=1346;AF=0.005201;SB=0;DP4=511,828,3,4 +NC_045512.2 24971 . G GT 61.0 PASS DP=1557;AF=0.002569;SB=12;DP4=820,770,0,4;INDEL;HRUN=3 +NC_045512.2 25703 . C CT 54.0 PASS DP=514;AF=0.005837;SB=5;DP4=451,60,2,1;INDEL;HRUN=4 +NC_045512.2 26094 . TA T 78.0 PASS DP=1369;AF=0.003652;SB=2;DP4=989,383,3,2;INDEL;HRUN=4 +NC_045512.2 26144 . G T 33850.0 PASS DP=1012;AF=0.951581;SB=0;DP4=0,1,491,519 +NC_045512.2 27175 . C CT 63.0 PASS DP=1388;AF=0.002882;SB=0;DP4=537,890,1,3;INDEL;HRUN=3 +NC_045512.2 27481 . C T 96.0 PASS DP=1915;AF=0.005222;SB=0;DP4=1454,450,8,2 +NC_045512.2 28147 . C CT 82.0 PASS DP=1104;AF=0.004529;SB=1;DP4=631,491,2,3;INDEL;HRUN=4 +NC_045512.2 28214 . C CT 307.0 PASS DP=876;AF=0.017123;SB=3;DP4=508,368,7,8;INDEL;HRUN=5 +NC_045512.2 28214 . C T 95.0 PASS DP=891;AF=0.008979;SB=1;DP4=511,372,4,4 +NC_045512.2 29003 . C A 70.0 PASS DP=953;AF=0.006296;SB=0;DP4=401,546,2,4 +NC_045512.2 29304 . C CA 108.0 PASS DP=1146;AF=0.005236;SB=3;DP4=727,416,5,1;INDEL;HRUN=3 +NC_045512.2 29386 . C T 84.0 PASS DP=1026;AF=0.006823;SB=12;DP4=639,380,7,0 +NC_045512.2 29679 . CT C 70.0 PASS DP=914;AF=0.004376;SB=2;DP4=177,738,1,3;INDEL;HRUN=3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.vcf Thu Jun 18 16:11:49 2020 -0400 @@ -0,0 +1,108 @@ +##fileformat=VCFv4.0 +##fileDate=20200606 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 50 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --def-alt-bq 0 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/008/613/8613450/working/pp-tmp/lofreq2_call_paralleltqdqbfki/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +##FILTER=<ID=min_snvqual_62,Description="Minimum SNV Quality (Phred) 62"> +##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50"> +##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10"> +##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> +##FILTER=<ID=min_snvqual_65,Description="Minimum SNV Quality (Phred) 65"> +##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53"> +##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf NC_045512.2 test-data/input.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 +NC_045512.2 105 . G T 3155.0 PASS DP=748;AF=0.171123;SB=0;DP4=600,20,124,4;ANN=T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.105G>T|||||| +NC_045512.2 443 . GT G 99.0 PASS DP=1286;AF=0.004666;SB=0;DP4=718,586,3,3;INDEL;HRUN=4;ANN=G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.182delT|p.Leu61fs|182/21291|182/21291|61/7096||INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.182delT|p.Leu61fs|182/540|182/540|61/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.182delT|p.Leu61fs|182/540|182/540|61/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.182delT|p.Leu61fs|182/13218|182/13218|61/4405||INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 507 . ATGGTCATGTTATGGT A 100.0 PASS DP=1554;AF=0.003861;SB=10;DP4=684,865,5,1;INDEL;HRUN=1;ANN=A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/21291|245/21291|82/7096||INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/540|245/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/540|245/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.245_259delGTCATGTTATGGTTG|p.Gly82_Val86del|245/13218|245/13218|82/4405||INFO_REALIGN_3_PRIME +NC_045512.2 509 . GGTCATGTTATGGTT G 99.0 PASS DP=1567;AF=0.003829;SB=0;DP4=706,873,3,3;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.246_259delTCATGTTATGGTTG|p.His83fs|246/21291|246/21291|82/7096||INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/540|246/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/540|246/540|82/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.246_259delTCATGTTATGGTTG|p.His83fs|246/13218|246/13218|82/4405||INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 514 . TGTTATG T 118.0 PASS DP=1696;AF=0.004127;SB=1;DP4=865,826,3,4;INDEL;HRUN=1;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.253_258delATGGTT|p.Met85_Val86del|253/21291|253/21291|85/7096||INFO_REALIGN_3_PRIME,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.253_258delATGGTT|p.Met85_Val86del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.253_258delATGGTT|p.Met85_Val86del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.253_258delATGGTT|p.Met85_Val86del|253/13218|253/13218|85/4405||INFO_REALIGN_3_PRIME +NC_045512.2 515 . GTTATGGTT G 59.0 PASS DP=1706;AF=0.002345;SB=4;DP4=887,826,1,3;INDEL;HRUN=2;ANN=G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.251_258delTTATGGTT|p.Val84fs|251/21291|251/21291|84/7096||,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.251_258delTTATGGTT|p.Val84fs|251/540|251/540|84/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.251_258delTTATGGTT|p.Val84fs|251/540|251/540|84/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.251_258delTTATGGTT|p.Val84fs|251/13218|251/13218|84/4405||;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 517 . TATG T 91.0 PASS DP=1733;AF=0.003462;SB=15;DP4=882,856,6,0;INDEL;HRUN=1;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.253_255delATG|p.Met85del|253/21291|253/21291|85/7096||,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.253_255delATG|p.Met85del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.253_255delATG|p.Met85del|253/540|253/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.253_255delATG|p.Met85del|253/13218|253/13218|85/4405|| +NC_045512.2 518 . ATG A 53.0 PASS DP=1679;AF=0.002382;SB=4;DP4=892,842,1,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.254_255delTG|p.Met85fs|254/21291|254/21291|85/7096||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.254_255delTG|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.254_255delTG|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.254_255delTG|p.Met85fs|254/13218|254/13218|85/4405||;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 518 . ATGGTT A 78.0 PASS DP=1679;AF=0.002978;SB=1;DP4=892,842,2,3;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.254_258delTGGTT|p.Met85fs|254/21291|254/21291|85/7096||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.254_258delTGGTT|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.254_258delTGGTT|p.Met85fs|254/540|254/540|85/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.254_258delTGGTT|p.Met85fs|254/13218|254/13218|85/4405||;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 685 . AAAGTCATTT A 60.0 PASS DP=1188;AF=0.003367;SB=2;DP4=607,618,1,3;INDEL;HRUN=3;ANN=A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/21291|421/21291|141/7096||,A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/540|421/540|141/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/540|421/540|141/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.421_429delAAGTCATTT|p.Lys141_Phe143del|421/13218|421/13218|141/4405|| +NC_045512.2 1011 . ATG A 77.0 PASS DP=1345;AF=0.003717;SB=1;DP4=927,454,3,2;INDEL;HRUN=1;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.747_748delTG|p.Tyr249fs|747/21291|747/21291|249/7096||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.747_748delTG|p.Tyr249fs|747/13218|747/13218|249/4405||,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.207_208delTG|p.Tyr69fs|207/1914|207/1914|69/637||WARNING_TRANSCRIPT_NO_START_CODON,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.207_208delTG|p.Tyr69fs|207/1914|207/1914|69/637||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 1135 . G GA 93.0 PASS DP=1272;AF=0.004717;SB=3;DP4=663,650,2,4;INDEL;HRUN=5;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.875dupA|p.Leu293fs|876/21291|876/21291|292/7096||INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.875dupA|p.Leu293fs|876/13218|876/13218|292/4405||INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.335dupA|p.Leu113fs|336/1914|336/1914|112/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.335dupA|p.Leu113fs|336/1914|336/1914|112/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.11) +NC_045512.2 1349 . C CA 257.0 PASS DP=1121;AF=0.011597;SB=1;DP4=444,668,6,7;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1088dupA|p.Asn363fs|1089/21291|1089/21291|363/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1088dupA|p.Asn363fs|1089/13218|1089/13218|363/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.548dupA|p.Asn183fs|549/1914|549/1914|183/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.548dupA|p.Asn183fs|549/1914|549/1914|183/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 1730 . G A 116.0 PASS DP=997;AF=0.009027;SB=2;DP4=440,548,5,4;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1465G>A|p.Glu489Lys|1465/21291|1465/21291|489/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1465G>A|p.Glu489Lys|1465/13218|1465/13218|489/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.925G>A|p.Glu309Lys|925/1914|925/1914|309/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.925G>A|p.Glu309Lys|925/1914|925/1914|309/637||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 1946 . G GT 206.0 PASS DP=1976;AF=0.006073;SB=0;DP4=982,986,6,6;INDEL;HRUN=4;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1685dupT|p.Leu562fs|1686/21291|1686/21291|562/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1685dupT|p.Leu562fs|1686/13218|1686/13218|562/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1145dupT|p.Leu382fs|1146/1914|1146/1914|382/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1145dupT|p.Leu382fs|1146/1914|1146/1914|382/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 2185 . G GT 73.0 PASS DP=2095;AF=0.002387;SB=4;DP4=1374,803,2,3;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1923dupT|p.Leu642fs|1924/21291|1924/21291|642/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1923dupT|p.Leu642fs|1924/13218|1924/13218|642/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1383dupT|p.Leu462fs|1384/1914|1384/1914|462/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1383dupT|p.Leu462fs|1384/1914|1384/1914|462/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 2310 . TA T 56.0 PASS DP=2134;AF=0.001874;SB=2;DP4=1056,1084,1,3;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2048delA|p.Asn683fs|2048/21291|2048/21291|683/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2048delA|p.Asn683fs|2048/13218|2048/13218|683/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1508delA|p.Asn503fs|1508/1914|1508/1914|503/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1508delA|p.Asn503fs|1508/1914|1508/1914|503/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 2480 . A G 49314.0 PASS DP=2088;AF=0.986590;SB=3;DP4=1,0,890,1196;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2215A>G|p.Ile739Val|2215/21291|2215/21291|739/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2215A>G|p.Ile739Val|2215/13218|2215/13218|739/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1675A>G|p.Ile559Val|1675/1914|1675/1914|559/637||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1675A>G|p.Ile559Val|1675/1914|1675/1914|559/637||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 2558 . C T 49314.0 PASS DP=2141;AF=0.983652;SB=0;DP4=0,1,736,1402;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2293C>T|p.Pro765Ser|2293/21291|2293/21291|765/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2293C>T|p.Pro765Ser|2293/13218|2293/13218|765/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1753C>T|p.Pro585Ser|1753/1914|1753/1914|585/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1753C>T|p.Pro585Ser|1753/1914|1753/1914|585/637||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 2612 . G GT 58.0 PASS DP=1770;AF=0.002260;SB=4;DP4=884,972,3,1;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2350dupT|p.Cys784fs|2351/21291|2351/21291|784/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2350dupT|p.Cys784fs|2351/13218|2351/13218|784/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1810dupT|p.Cys604fs|1811/1914|1811/1914|604/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1810dupT|p.Cys604fs|1811/1914|1811/1914|604/637||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3259 . G T 69.0 PASS DP=1704;AF=0.004108;SB=25;DP4=723,974,7,0;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2994G>T|p.Gln998His|2994/21291|2994/21291|998/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2994G>T|p.Gln998His|2994/13218|2994/13218|998/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.540G>T|p.Gln180His|540/5835|540/5835|180/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.540G>T|p.Gln180His|540/5835|540/5835|180/1944||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 3412 . T TA 69.0 PASS DP=1670;AF=0.002994;SB=0;DP4=803,866,2,3;INDEL;HRUN=5;ANN=TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3152dupA|p.Val1052fs|3153/21291|3153/21291|1051/7096||INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3152dupA|p.Val1052fs|3153/13218|3153/13218|1051/4405||INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.698dupA|p.Val234fs|699/5835|699/5835|233/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,TA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.698dupA|p.Val234fs|699/5835|699/5835|233/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3448 . C CA 59.0 PASS DP=1732;AF=0.002309;SB=0;DP4=733,997,2,2;INDEL;HRUN=2;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3185dupA|p.Asn1062fs|3186/21291|3186/21291|1062/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3185dupA|p.Asn1062fs|3186/13218|3186/13218|1062/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.731dupA|p.Asn244fs|732/5835|732/5835|244/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.731dupA|p.Asn244fs|732/5835|732/5835|244/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 3545 . AATG A 57.0 PASS DP=2002;AF=0.001998;SB=4;DP4=945,1062,3,1;INDEL;HRUN=2;ANN=A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3281_3283delATG|p.Asn1094_Gly1095delinsArg|3281/21291|3281/21291|1094/7096||,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3281_3283delATG|p.Asn1094_Gly1095delinsArg|3281/13218|3281/13218|1094/4405||,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.827_829delATG|p.Asn276_Gly277delinsArg|827/5835|827/5835|276/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.827_829delATG|p.Asn276_Gly277delinsArg|827/5835|827/5835|276/1944||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 4148 . G GT 63.0 PASS DP=1147;AF=0.003487;SB=1;DP4=474,683,1,3;INDEL;HRUN=4;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3887dupT|p.Leu1296fs|3888/21291|3888/21291|1296/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3887dupT|p.Leu1296fs|3888/13218|3888/13218|1296/4405||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1433dupT|p.Leu478fs|1434/5835|1434/5835|478/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1433dupT|p.Leu478fs|1434/5835|1434/5835|478/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6287 . TG T 60.0 PASS DP=1537;AF=0.002602;SB=2;DP4=810,729,3,1;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6024delG|p.Trp2008fs|6024/21291|6024/21291|2008/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6024delG|p.Trp2008fs|6024/13218|6024/13218|2008/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3570delG|p.Trp1190fs|3570/5835|3570/5835|1190/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3570delG|p.Trp1190fs|3570/5835|3570/5835|1190/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6696 . C CT 1002.0 PASS DP=1985;AF=0.022670;SB=1;DP4=739,1238,18,27;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6435dupT|p.Leu2146fs|6436/21291|6436/21291|2146/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6435dupT|p.Leu2146fs|6436/13218|6436/13218|2146/4405||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3981dupT|p.Leu1328fs|3982/5835|3982/5835|1328/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3981dupT|p.Leu1328fs|3982/5835|3982/5835|1328/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 6696 . C T 141.0 PASS DP=2023;AF=0.006920;SB=0;DP4=752,1256,5,10;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6431C>T|p.Pro2144Leu|6431/21291|6431/21291|2144/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6431C>T|p.Pro2144Leu|6431/13218|6431/13218|2144/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3977C>T|p.Pro1326Leu|3977/5835|3977/5835|1326/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3977C>T|p.Pro1326Leu|3977/5835|3977/5835|1326/1944||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 7504 . C CA 57.0 PASS DP=1874;AF=0.002134;SB=0;DP4=990,903,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7242dupA|p.Arg2415fs|7243/21291|7243/21291|2415/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7242dupA|p.Arg2415fs|7243/13218|7243/13218|2415/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4788dupA|p.Arg1597fs|4789/5835|4789/5835|1597/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4788dupA|p.Arg1597fs|4789/5835|4789/5835|1597/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 9118 . C T 170.0 PASS DP=2259;AF=0.006640;SB=14;DP4=1213,1031,4,11;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8853C>T|p.Asp2951Asp|8853/21291|8853/21291|2951/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8853C>T|p.Asp2951Asp|8853/13218|8853/13218|2951/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.564C>T|p.Asp188Asp|564/1500|564/1500|188/499||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.564C>T|p.Asp188Asp|564/1500|564/1500|188/499||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 9502 . C T 221.0 PASS DP=2082;AF=0.009606;SB=0;DP4=836,1225,8,12;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9237C>T|p.Ala3079Ala|9237/21291|9237/21291|3079/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9237C>T|p.Ala3079Ala|9237/13218|9237/13218|3079/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.948C>T|p.Ala316Ala|948/1500|948/1500|316/499||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.948C>T|p.Ala316Ala|948/1500|948/1500|316/499||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 9701 . AT A 59.0 PASS DP=1741;AF=0.002298;SB=2;DP4=843,930,1,3;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9439delT|p.Cys3147fs|9439/21291|9439/21291|3147/7096||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9439delT|p.Cys3147fs|9439/13218|9439/13218|3147/4405||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1150delT|p.Cys384fs|1150/1500|1150/1500|384/499||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1150delT|p.Cys384fs|1150/1500|1150/1500|384/499||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10605 . C CT 116.0 PASS DP=2586;AF=0.003094;SB=0;DP4=1507,1082,5,3;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10344dupT|p.Val3449fs|10345/21291|10345/21291|3449/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10344dupT|p.Val3449fs|10345/13218|10345/13218|3449/4405||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.555dupT|p.Val186fs|556/918|556/918|186/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.555dupT|p.Val186fs|556/918|556/918|186/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 10619 . C A 235.0 PASS DP=2564;AF=0.007800;SB=5;DP4=1272,1272,7,13;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10354C>A|p.Gln3452Lys|10354/21291|10354/21291|3452/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10354C>A|p.Gln3452Lys|10354/13218|10354/13218|3452/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.565C>A|p.Gln189Lys|565/918|565/918|189/305||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.565C>A|p.Gln189Lys|565/918|565/918|189/305||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 10660 . TA T 122.0 PASS DP=2326;AF=0.003439;SB=15;DP4=1292,1057,1,7;INDEL;HRUN=2;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10397delA|p.Asn3466fs|10397/21291|10397/21291|3466/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10397delA|p.Asn3466fs|10397/13218|10397/13218|3466/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.608delA|p.Asn203fs|608/918|608/918|203/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.608delA|p.Asn203fs|608/918|608/918|203/305||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11074 . C CT 281.0 PASS DP=1459;AF=0.036326;SB=2;DP4=822,613,28,25;INDEL;HRUN=8;ANN=CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817dupT|p.Leu3606fs|10818/21291|10818/21291|3606/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10817dupT|p.Leu3606fs|10818/13218|10818/13218|3606/4405||INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.110dupT|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.110dupT|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11082 . TG T 1843.0 PASS DP=1309;AF=0.058060;SB=0;DP4=662,589,39,37;INDEL;HRUN=1;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10818delG|p.Leu3606fs|10818/21291|10818/21291|3606/7096||,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10818delG|p.Leu3606fs|10818/13218|10818/13218|3606/4405||,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.111delG|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.111delG|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11083 . G T 39536.0 PASS DP=1319;AF=0.918120;SB=0;DP4=0,0,645,595;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10818G>T|p.Leu3606Phe|10818/21291|10818/21291|3606/7096||,T|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||,T|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,T|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 +NC_045512.2 11133 . CT C 60.0 PASS DP=1181;AF=0.003387;SB=2;DP4=607,573,3,1;INDEL;HRUN=4;ANN=C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10872delT|p.Phe3624fs|10872/21291|10872/21291|3624/7096||INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10872delT|p.Phe3624fs|10872/13218|10872/13218|3624/4405||INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.165delT|p.Phe55fs|165/870|165/870|55/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,C|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.165delT|p.Phe55fs|165/870|165/870|55/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11301 . TA T 104.0 PASS DP=2098;AF=0.003337;SB=9;DP4=796,1299,5,2;INDEL;HRUN=4;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11040delA|p.Asp3681fs|11040/21291|11040/21291|3680/7096||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11040delA|p.Asp3681fs|11040/13218|11040/13218|3680/4405||INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.333delA|p.Asp112fs|333/870|333/870|111/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.333delA|p.Asp112fs|333/870|333/870|111/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 11812 . C CA 215.0 PASS DP=2020;AF=0.005941;SB=0;DP4=891,1127,5,7;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11550dupA|p.Pro3851fs|11551/21291|11551/21291|3851/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11550dupA|p.Pro3851fs|11551/13218|11551/13218|3851/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.843dupA|p.Pro282fs|844/870|844/870|282/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.843dupA|p.Pro282fs|844/870|844/870|282/289||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 11812 . C A 104.0 PASS DP=2030;AF=0.004926;SB=13;DP4=895,1123,1,9;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11547C>A|p.Gly3849Gly|11547/21291|11547/21291|3849/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11547C>A|p.Gly3849Gly|11547/13218|11547/13218|3849/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.840C>A|p.Gly280Gly|840/870|840/870|280/289||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.840C>A|p.Gly280Gly|840/870|840/870|280/289||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 12296 . C CA 222.0 PASS DP=1709;AF=0.007022;SB=6;DP4=573,1131,6,6;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12034dupA|p.Met4012fs|12035/21291|12035/21291|4012/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12034dupA|p.Met4012fs|12035/13218|12035/13218|4012/4405||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.208dupA|p.Met70fs|209/594|209/594|70/197||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.208dupA|p.Met70fs|209/594|209/594|70/197||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.14) +NC_045512.2 14110 . C CA 57.0 PASS DP=1940;AF=0.002062;SB=0;DP4=872,1128,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13849dupA|p.Thr4617fs|13850/21291|13850/21291|4617/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.673dupA|p.Thr225fs|674/2796|674/2796|225/931||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 14205 . A C 790.0 PASS DP=2047;AF=0.023449;SB=38;DP4=1106,890,41,9;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13941A>C|p.Ser4647Ser|13941/21291|13941/21291|4647/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.765A>C|p.Ser255Ser|765/2796|765/2796|255/931||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 14327 . C CA 59.0 PASS DP=1729;AF=0.002313;SB=0;DP4=693,1040,2,2;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14066dupA|p.Asn4689fs|14067/21291|14067/21291|4689/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.890dupA|p.Asn297fs|891/2796|891/2796|297/931||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 14432 . G GA 118.0 PASS DP=1895;AF=0.004222;SB=3;DP4=1004,913,3,5;INDEL;HRUN=5;ANN=GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14173dupA|p.Ile4725fs|14174/21291|14174/21291|4725/7096||INFO_REALIGN_3_PRIME,GA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.997dupA|p.Ile333fs|998/2796|998/2796|333/931||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 14625 . C T 78.0 PASS DP=2695;AF=0.003340;SB=3;DP4=2134,550,7,3;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14361C>T|p.Cys4787Cys|14361/21291|14361/21291|4787/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1185C>T|p.Cys395Cys|1185/2796|1185/2796|395/931||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 14745 . TGAATTA T 111.0 PASS DP=2063;AF=0.003393;SB=8;DP4=975,1086,1,6;INDEL;HRUN=1;ANN=T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14482_14487delGAATTA|p.Glu4828_Leu4829del|14482/21291|14482/21291|4828/7096||,T|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1306_1311delGAATTA|p.Glu436_Leu437del|1306/2796|1306/2796|436/931||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 14805 . C T 49314.0 PASS DP=2660;AF=0.987594;SB=0;DP4=0,0,1259,1398;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 +NC_045512.2 14852 . TTGTA T 67.0 PASS DP=2763;AF=0.001810;SB=1;DP4=1578,1259,2,3;INDEL;HRUN=3;ANN=T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14589_14592delTGTA|p.Phe4863fs|14589/21291|14589/21291|4863/7096||,T|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1413_1416delTGTA|p.Phe471fs|1413/2796|1413/2796|471/931||WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 17916 . AT A 53.0 PASS DP=2304;AF=0.001736;SB=4;DP4=1310,1011,1,3;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17655delT|p.Phe5885fs|17655/21291|17655/21291|5885/7096||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1683delT|p.Phe561fs|1683/1803|1683/1803|561/600||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 18350 . ATTTACC A 57.0 PASS DP=1950;AF=0.002051;SB=0;DP4=974,1048,2,2;INDEL;HRUN=3;ANN=A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18092_18097delCTTTAC|p.Pro6031_Leu6032del|18092/21291|18092/21291|6031/7096||INFO_REALIGN_3_PRIME,A|disruptive_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.317_322delCTTTAC|p.Pro106_Leu107del|317/1581|317/1581|106/526||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME +NC_045512.2 18688 . T C 93.0 PASS DP=1875;AF=0.005333;SB=9;DP4=938,925,8,2;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18424T>C|p.Phe6142Leu|18424/21291|18424/21291|6142/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.649T>C|p.Phe217Leu|649/1581|649/1581|217/526||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 19017 . C T 86.0 PASS DP=2058;AF=0.004373;SB=1;DP4=910,1138,3,6;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18753C>T|p.Phe6251Phe|18753/21291|18753/21291|6251/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.978C>T|p.Phe326Phe|978/1581|978/1581|326/526||WARNING_TRANSCRIPT_NO_START_CODON +NC_045512.2 19188 . A AT 55.0 PASS DP=1835;AF=0.002180;SB=5;DP4=769,1067,3,1;INDEL;HRUN=4;ANN=AT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18928dupT|p.Trp6310fs|18929/21291|18929/21291|6310/7096||INFO_REALIGN_3_PRIME,AT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1153dupT|p.Trp385fs|1154/1581|1154/1581|385/526||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 19983 . C CT 137.0 PASS DP=1533;AF=0.007828;SB=0;DP4=652,888,5,7;INDEL;HRUN=6;ANN=CT|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19725dupT|p.Asp6576fs|19726/21291|19726/21291|6576/7096||INFO_REALIGN_3_PRIME,CT|frameshift_variant&stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.369dupT|p.Asp124fs|370/1038|370/1038|124/345||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 20091 . C CA 81.0 PASS DP=1477;AF=0.003385;SB=4;DP4=814,661,4,1;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19830dupA|p.Gln6611fs|19831/21291|19831/21291|6611/7096||INFO_REALIGN_3_PRIME,CA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.474dupA|p.Gln159fs|475/1038|475/1038|159/345||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 20296 . AAATT A 64.0 PASS DP=1333;AF=0.003001;SB=2;DP4=423,909,2,2;INDEL;HRUN=3;ANN=A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20034_20037delATTA|p.Leu6679fs|20034/21291|20034/21291|6678/7096||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.678_681delATTA|p.Leu227fs|678/1038|678/1038|226/345||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.07) +NC_045512.2 20890 . G GT 63.0 PASS DP=1405;AF=0.002847;SB=2;DP4=957,485,2,2;INDEL;HRUN=2;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20628dupT|p.Ala6877fs|20629/21291|20629/21291|6877/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.234dupT|p.Ala79fs|235/894|235/894|79/297||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 21101 . G GT 105.0 PASS DP=1133;AF=0.007944;SB=1;DP4=525,606,5,4;INDEL;HRUN=6;ANN=GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20843dupT|p.Thr6949fs|20844/21291|20844/21291|6948/7096||INFO_REALIGN_3_PRIME,GT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.449dupT|p.Thr151fs|450/894|450/894|150/297||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME;LOF=(ORF1ab|GU280_gp01|28|0.04) +NC_045512.2 22383 . C CT 64.0 PASS DP=978;AF=0.004090;SB=4;DP4=454,598,3,1;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.825dupT|p.Leu276fs|826/3822|826/3822|276/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22583 . G GT 124.0 PASS DP=874;AF=0.008009;SB=0;DP4=472,402,4,3;INDEL;HRUN=5;ANN=GT|frameshift_variant&stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1026dupT|p.Asn343fs|1027/3822|1027/3822|343/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 22802 . C CA 87.0 PASS DP=1083;AF=0.004617;SB=1;DP4=646,483,2,3;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1243dupA|p.Thr415fs|1244/3822|1244/3822|415/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23191 . C T 5808.0 PASS DP=1605;AF=0.149533;SB=8;DP4=895,464,150,96;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1629C>T|p.Phe543Phe|1629/3822|1629/3822|543/1273|| +NC_045512.2 23568 . GTA G 66.0 PASS DP=2956;AF=0.001691;SB=1;DP4=1354,1607,3,2;INDEL;HRUN=1;ANN=G|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2010_2011delAT|p.Ile670fs|2010/3822|2010/3822|670/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23621 . G A 76.0 PASS DP=2968;AF=0.003032;SB=1;DP4=1090,1868,4,5;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2059G>A|p.Val687Ile|2059/3822|2059/3822|687/1273|| +NC_045512.2 23735 . G GA 53.0 PASS DP=2490;AF=0.001606;SB=0;DP4=629,1866,1,3;INDEL;HRUN=3;ANN=GA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2176dupA|p.Ile726fs|2177/3822|2177/3822|726/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 23835 . G GT 71.0 PASS DP=1518;AF=0.003294;SB=4;DP4=924,620,2,3;INDEL;HRUN=5;ANN=GT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2278dupT|p.Cys760fs|2279/3822|2279/3822|760/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 24025 . ACTT A 76.0 PASS DP=1327;AF=0.003768;SB=4;DP4=523,808,3,2;INDEL;HRUN=1;ANN=A|conservative_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2464_2466delCTT|p.Leu822del|2464/3822|2464/3822|822/1273|| +NC_045512.2 24358 . C CA 80.0 PASS DP=1275;AF=0.003922;SB=1;DP4=861,420,3,2;INDEL;HRUN=4;ANN=CA|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2800dupA|p.Ile934fs|2801/3822|2801/3822|934/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 24858 . G A 74.0 PASS DP=1346;AF=0.005201;SB=0;DP4=511,828,3,4;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3296G>A|p.Gly1099Asp|3296/3822|3296/3822|1099/1273|| +NC_045512.2 24971 . G GT 61.0 PASS DP=1557;AF=0.002569;SB=12;DP4=820,770,0,4;INDEL;HRUN=3;ANN=GT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3412dupT|p.Tyr1138fs|3413/3822|3413/3822|1138/1273||INFO_REALIGN_3_PRIME;LOF=(S|GU280_gp02|1|1.00) +NC_045512.2 25703 . C CT 54.0 PASS DP=514;AF=0.005837;SB=5;DP4=451,60,2,1;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.315dupT|p.Leu106fs|316/828|316/828|106/275||INFO_REALIGN_3_PRIME;LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 26094 . TA T 78.0 PASS DP=1369;AF=0.003652;SB=2;DP4=989,383,3,2;INDEL;HRUN=4;ANN=T|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.706delA|p.Ile236fs|706/828|706/828|236/275||INFO_REALIGN_3_PRIME;LOF=(ORF3a|GU280_gp03|1|1.00) +NC_045512.2 26144 . G T 33850.0 PASS DP=1012;AF=0.951581;SB=0;DP4=0,1,491,519;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.752G>T|p.Gly251Val|752/828|752/828|251/275|| +NC_045512.2 27175 . C CT 63.0 PASS DP=1388;AF=0.002882;SB=0;DP4=537,890,1,3;INDEL;HRUN=3;ANN=CT|frameshift_variant|HIGH|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.656dupT|p.Leu219fs|657/669|657/669|219/222||INFO_REALIGN_3_PRIME +NC_045512.2 27481 . C T 96.0 PASS DP=1915;AF=0.005222;SB=0;DP4=1454,450,8,2;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.88C>T|p.Leu30Phe|88/366|88/366|30/121|| +NC_045512.2 28147 . C CT 82.0 PASS DP=1104;AF=0.004529;SB=1;DP4=631,491,2,3;INDEL;HRUN=4;ANN=CT|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.258dupT|p.Thr87fs|259/366|259/366|87/121||INFO_REALIGN_3_PRIME;LOF=(ORF8|GU280_gp09|1|1.00) +NC_045512.2 28214 . C CT 307.0 PASS DP=876;AF=0.017123;SB=3;DP4=508,368,7,8;INDEL;HRUN=5;ANN=CT|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.326dupT|p.Leu109fs|327/366|327/366|109/121||INFO_REALIGN_3_PRIME;LOF=(ORF8|GU280_gp09|1|1.00) +NC_045512.2 28214 . C T 95.0 PASS DP=891;AF=0.008979;SB=1;DP4=511,372,4,4;ANN=T|synonymous_variant|LOW|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.321C>T|p.Asp107Asp|321/366|321/366|107/121|| +NC_045512.2 29003 . C A 70.0 PASS DP=953;AF=0.006296;SB=0;DP4=401,546,2,4;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.730C>A|p.Gln244Lys|730/1260|730/1260|244/419|| +NC_045512.2 29304 . C CA 108.0 PASS DP=1146;AF=0.005236;SB=3;DP4=727,416,5,1;INDEL;HRUN=3;ANN=CA|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1034dupA|p.Asn345fs|1035/1260|1035/1260|345/419||INFO_REALIGN_3_PRIME;LOF=(N|GU280_gp10|1|1.00) +NC_045512.2 29386 . C T 84.0 PASS DP=1026;AF=0.006823;SB=12;DP4=639,380,7,0;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1113C>T|p.Asp371Asp|1113/1260|1113/1260|371/419|| +NC_045512.2 29679 . CT C 70.0 PASS DP=914;AF=0.004376;SB=2;DP4=177,738,1,3;INDEL;HRUN=3;ANN=C|intergenic_region|MODIFIER|ORF10-CHR_END|GU280_gp11-CHR_END|intergenic_region|GU280_gp11-CHR_END|||n.29680delT||||||