Mercurial > repos > iuc > virheat
view test-data/day_85.vcf @ 0:d2a1ac520392 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit ed302b5ddedadffc87798b7216f1a331accce96e
| author | iuc |
|---|---|
| date | Wed, 15 May 2024 13:37:49 +0000 |
| parents | |
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##fileformat=VCFv4.0 ##fileDate=20220927 ##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/996/50996339/tmp/lofreq2_call_parallel_00t3eed/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_68,Description="Minimum SNV Quality (Phred) 68"> ##FILTER=<ID=min_indelqual_52,Description="Minimum Indel Quality (Phred) 52"> ##FILTER=<ID=min_snvqual_75,Description="Minimum SNV Quality (Phred) 75"> ##FILTER=<ID=min_indelqual_60,Description="Minimum Indel Quality (Phred) 60"> ##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000"> ##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20"> ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> ##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" ##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/996/50996574/outputs/galaxy_dataset_61c05207-723c-481f-a33c-93acf8a6685f.dat -csvStats /data/jwd01/main/050/996/50996574/outputs/galaxy_dataset_609dc569-c14e-4725-861e-c0faa56ea1a3.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/3/d/e/dataset_3dec9a4b-cd72-4350-9252-e3ac4947f31b.dat " ##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' "> ##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 509 . GGTCATGTTA G 24816.0 PASS AF=0.969084;DP=841;DP4=72,85,462,353;HRUN=2;SB=18;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 670 . T G 25606.0 PASS AF=0.942105;DP=760;DP4=1,0,393,363;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 900 . C T 49314.0 PASS AF=0.949125;DP=1828;DP4=2,2,914,905;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 1980 . G T 10608.0 PASS AF=0.895062;DP=324;DP4=0,3,167,153;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 2790 . C T 11585.0 PASS AF=0.924419;DP=344;DP4=0,0,172,170;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 3037 . C T 32298.0 PASS AF=0.957929;DP=927;DP4=1,2,464,457;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4184 . G A 17648.0 PASS AF=0.933464;DP=511;DP4=0,0,288,218;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 4276 . C T 14453.0 PASS AF=0.856838;DP=468;DP4=0,0,358,106;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4321 . C T 4973.0 PASS AF=0.407229;DP=415;DP4=233,1,92,89;SB=373;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 5302 . A G 2648.0 PASS AF=0.153736;DP=696;DP4=281,288,58,66;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 5628 . C T 14736.0 PASS AF=0.923077;DP=442;DP4=2,2,214,221;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 6354 . C T 9316.0 PASS AF=0.575453;DP=497;DP4=194,0,181,121;SB=310;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9344 . C T 21975.0 PASS AF=0.939778;DP=631;DP4=0,0,309,319;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9424 . A G 20883.0 PASS AF=0.922204;DP=617;DP4=0,1,312,300;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 9534 . C T 44514.0 PASS AF=0.894855;DP=1341;DP4=1,0,686,648;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9866 . C T 31818.0 PASS AF=0.954190;DP=895;DP4=1,1,504,388;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10029 . C T 40172.0 PASS AF=0.923801;DP=1168;DP4=0,0,542,624;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10198 . C T 19006.0 PASS AF=0.917563;DP=558;DP4=0,0,290,264;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10447 . G A 14949.0 PASS AF=0.899329;DP=447;DP4=0,0,220,225;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 10449 . C A 14477.0 PASS AF=0.861538;DP=455;DP4=4,11,222,217;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 11287 . GTCTGGTTTT G 8782.0 PASS AF=0.975694;DP=288;DP4=30,31,138,143;HRUN=1;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 12036 . C T 20280.0 PASS AF=0.917742;DP=620;DP4=1,1,282,333;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 12854 . C T 14821.0 PASS AF=0.845992;DP=474;DP4=0,6,234,233;SB=15;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 12880 . C T 17325.0 PASS AF=0.968685;DP=479;DP4=0,1,232,246;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 14408 . C T 49314.0 PASS AF=0.949393;DP=1482;DP4=0,3,709,768;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 15451 . G A 36768.0 PASS AF=0.911172;DP=1092;DP4=1,0,606,468;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A) NC_045512 15714 . C T 21744.0 PASS AF=0.948136;DP=617;DP4=1,3,318,293;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 17410 . C T 7745.0 PASS AF=0.928889;DP=225;DP4=0,0,107,117;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 18163 . A G 13119.0 PASS AF=0.891626;DP=406;DP4=1,1,199,203;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G) NC_045512 19955 . C T 49314.0 PASS AF=0.947122;DP=1494;DP4=0,0,747,741;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 20055 . A G 10686.0 PASS AF=0.902141;DP=327;DP4=20,0,148,159;SB=59;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G) NC_045512 20719 . C T 10811.0 PASS AF=0.932692;DP=312;DP4=1,2,166,141;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 21618 . C T 37364.0 PASS AF=0.888987;DP=1135;DP4=0,6,560,553;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 21632 . TTACCCCCTG T 32441.0 PASS AF=0.980080;DP=1004;DP4=55,42,469,515;HRUN=2;SB=9;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 21987 . G A 36002.0 PASS AF=0.907493;DP=1081;DP4=0,1,557,519;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22200 . T G 16165.0 PASS AF=0.924843;DP=479;DP4=3,0,211,263;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22578 . G A 19580.0 PASS AF=0.824508;DP=661;DP4=0,0,301,343;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22599 . G C 20362.0 PASS AF=0.902280;DP=614;DP4=0,0,300,306;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22629 . A C 19818.0 PASS AF=0.902156;DP=603;DP4=0,1,307,293;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22664 . C A 18689.0 PASS AF=0.893428;DP=563;DP4=2,1,281,277;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22674 . C T 18845.0 PASS AF=0.926916;DP=561;DP4=0,0,275,284;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22679 . T C 19011.0 PASS AF=0.926056;DP=568;DP4=1,0,288,278;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22686 . C T 17628.0 PASS AF=0.950851;DP=529;DP4=0,3,273,253;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22688 . A G 16023.0 PASS AF=0.869141;DP=512;DP4=0,1,269,238;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22716 . C T 19370.0 PASS AF=0.939068;DP=558;DP4=0,0,301,254;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22775 . G A 49314.0 PASS AF=0.797604;DP=2337;DP4=173,208,921,1033;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22786 . A C 49314.0 PASS AF=0.895996;DP=1923;DP4=4,10,908,996;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22792 . C T 49314.0 PASS AF=0.946617;DP=1892;DP4=0,1,900,987;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22813 . G T 49314.0 PASS AF=0.922457;DP=1986;DP4=2,1,957,1014;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22882 . T G 37187.0 PASS AF=0.825487;DP=1232;DP4=5,2,668,550;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22992 . G A 39520.0 PASS AF=0.943478;DP=1150;DP4=0,0,533,607;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22995 . C A 41015.0 PASS AF=0.971831;DP=1136;DP4=0,0,539,597;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23013 . A C 39263.0 PASS AF=0.911243;DP=1183;DP4=7,7,556,609;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 23040 . A G 38673.0 PASS AF=0.916594;DP=1151;DP4=2,5,543,597;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23055 . A G 35683.0 PASS AF=0.902992;DP=1103;DP4=2,2,535,559;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23063 . A T 37185.0 PASS AF=0.957733;DP=1041;DP4=0,0,521,520;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 23075 . T C 33766.0 PASS AF=0.872827;DP=1093;DP4=5,2,561,522;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 23403 . A G 13054.0 PASS AF=0.951743;DP=373;DP4=0,1,178,194;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23525 . C T 10850.0 PASS AF=0.873900;DP=341;DP4=1,0,165,171;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 23599 . T G 44250.0 PASS AF=0.941223;DP=1276;DP4=3,1,664,607;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23604 . C A 41230.0 PASS AF=0.902244;DP=1248;DP4=0,0,651,595;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23781 . T C 24650.0 PASS AF=0.918256;DP=734;DP4=0,0,354,379;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 23854 . C A 18022.0 PASS AF=0.911071;DP=551;DP4=0,3,263,285;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23948 . G T 18412.0 PASS AF=0.883929;DP=560;DP4=0,0,271,284;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 24424 . A T 44012.0 PASS AF=0.835790;DP=1425;DP4=6,32,729,656;SB=53;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 24469 . T A 49314.0 PASS AF=0.941802;DP=1598;DP4=4,0,824,765;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 24966 . A G 25737.0 PASS AF=0.916237;DP=776;DP4=0,4,362,405;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 25000 . C T 23128.0 PASS AF=0.932836;DP=670;DP4=0,0,336,332;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 25584 . C T 34714.0 PASS AF=0.843556;DP=1125;DP4=1,17,617,486;SB=49;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26060 . C T 48795.0 PASS AF=0.959004;DP=1366;DP4=0,2,689,673;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26195 . C T 17410.0 PASS AF=0.867621;DP=559;DP4=0,1,274,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26270 . C T 16029.0 PASS AF=0.877264;DP=497;DP4=1,1,252,235;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512 26408 . C T 37918.0 PASS AF=0.924915;DP=1172;DP4=0,0,574,561;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512 26577 . C G 23695.0 PASS AF=0.921316;DP=699;DP4=1,0,337,354;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512 26709 . G A 49314.0 PASS AF=0.946639;DP=1443;DP4=0,0,767,673;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512 26801 . C T 47205.0 PASS AF=0.941005;DP=1373;DP4=2,1,682,684;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 26858 . C T 41810.0 PASS AF=0.962835;DP=1157;DP4=0,0,532,623;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 27259 . A C 49314.0 PASS AF=0.903539;DP=1752;DP4=0,4,732,1001;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27382 . G C 16412.0 PASS AF=0.903292;DP=486;DP4=1,0,237,242;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27383 . A T 15885.0 PASS AF=0.877083;DP=480;DP4=0,1,238,233;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512 27384 . T C 16182.0 PASS AF=0.877800;DP=491;DP4=1,0,245,242;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27481 . C A 21747.0 PASS AF=0.949429;DP=613;DP4=1,2,314,294;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A) NC_045512 27549 . C T 49314.0 PASS AF=0.901484;DP=1482;DP4=0,0,746,720;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) NC_045512 27807 . C T 16022.0 PASS AF=0.916143;DP=477;DP4=1,0,240,234;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T) NC_045512 28271 . A T 49314.0 PASS AF=0.923592;DP=1793;DP4=1,10,893,886;SB=19 NC_045512 28307 . G A 49314.0 PASS AF=0.852097;DP=1812;DP4=3,2,884,890;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28311 . C T 49314.0 PASS AF=0.829309;DP=1781;DP4=5,24,875,873;SB=32;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512 28361 . GGAGAACGCA G 40362.0 PASS AF=0.788374;DP=1531;DP4=239,97,491,716;HRUN=2;SB=226;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME) NC_045512 28483 . A G 24535.0 PASS AF=0.917663;DP=753;DP4=3,4,354,387;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G) NC_045512 28657 . C T 49314.0 PASS AF=0.927105;DP=1948;DP4=3,2,1064,862;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512 28881 . G A 29591.0 PASS AF=0.964242;DP=811;DP4=0,1,411,397;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28882 . G A 27445.0 PASS AF=0.918216;DP=807;DP4=0,1,408,394;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28883 . G C 27530.0 PASS AF=0.907317;DP=820;DP4=2,0,413,402;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512 29510 . A C 49314.0 PASS AF=0.902691;DP=1932;DP4=1,1,877,1050;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C) NC_045512 29733 . CGAGGCCACGCGGAGTACGATCGAGTG C 30334.0 PASS AF=0.994702;DP=755;DP4=144,132,273,478;HRUN=1;SB=52;INDEL