Mercurial > repos > iuc > virheat
view test-data/day_2.vcf @ 1:30584e80d61e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
| author | iuc |
|---|---|
| date | Mon, 03 Jun 2024 09:37:09 +0000 |
| parents | d2a1ac520392 |
| children |
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##fileformat=VCFv4.0 ##fileDate=20220906 ##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/050/269/50269463/tmp/lofreq2_call_parallelzjjfw9e7/0.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_66,Description="Minimum SNV Quality (Phred) 66"> ##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50"> ##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74"> ##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58"> ##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/050/269/50269698/outputs/galaxy_dataset_88addf3f-f2e4-4637-81e0-e43aa1e91417.dat -csvStats /data/jwd01/main/050/269/50269698/outputs/galaxy_dataset_17b38e29-aa4a-4ae7-bdbe-12272452464e.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/9/e/f/dataset_9ef6f377-a1fd-48d3-99c0-cb0477d7ba5f.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 49314.0 PASS AF=0.969960;DP=1731;DP4=78,84,956,723;HRUN=2;SB=14;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 40246.0 PASS AF=0.935565;DP=1195;DP4=0,0,610,585;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 761 . A G 13864.0 PASS AF=0.362500;DP=1280;DP4=392,394,250,242;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agc/Ggc|S166G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 900 . C T 49314.0 PASS AF=0.943740;DP=1813;DP4=1,1,892,917;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 13418.0 PASS AF=0.893035;DP=402;DP4=1,0,199,199;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 2790 . C T 15400.0 PASS AF=0.933333;DP=450;DP4=0,0,227,220;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 27805.0 PASS AF=0.945980;DP=796;DP4=2,2,395,394;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4184 . G A 8444.0 PASS AF=0.915323;DP=248;DP4=0,0,149,98;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 4321 . C T 7289.0 PASS AF=0.692064;DP=315;DP4=80,3,123,108;SB=139;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 5365 . C T 7054.0 PASS AF=0.291717;DP=833;DP4=171,380,130,146;SB=50;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1700|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 6318 . C T 6698.0 PASS AF=0.314865;DP=740;DP4=230,256,116,137;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCa/cTa|P2018L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9344 . C T 26982.0 PASS AF=0.967742;DP=744;DP4=0,0,370,374;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 24944.0 PASS AF=0.929444;DP=737;DP4=1,0,378,357;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 9534 . C T 47610.0 PASS AF=0.951347;DP=1336;DP4=0,1,643,690;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 19843.0 PASS AF=0.965642;DP=553;DP4=0,0,325,228;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9930 . A G 3433.0 PASS AF=0.139558;DP=996;DP4=417,414,86,74;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3222G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 10029 . C T 34725.0 PASS AF=0.801016;DP=1181;DP4=0,5,554,616;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10198 . C T 23131.0 PASS AF=0.922059;DP=680;DP4=1,0,352,325;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10447 . G A 21620.0 PASS AF=0.906396;DP=641;DP4=0,0,325,311;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 10449 . C A 21547.0 PASS AF=0.903276;DP=641;DP4=1,0,331,308;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 10733 . C T 7258.0 PASS AF=0.211905;DP=1260;DP4=491,486,145,137;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3490F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 11287 . GTCTGGTTTT G 10490.0 PASS AF=0.985423;DP=343;DP4=18,23,167,171;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 12854 . C T 6207.0 PASS AF=0.371025;DP=566;DP4=183,149,131,102;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 12880 . C T 21798.0 PASS AF=0.968386;DP=601;DP4=0,0,307,294;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=0.945901;DP=1793;DP4=1,0,868,924;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 15714 . C T 26016.0 PASS AF=0.940860;DP=744;DP4=0,1,355,385;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 17410 . C T 8707.0 PASS AF=0.922780;DP=259;DP4=0,0,128,130;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 14458.0 PASS AF=0.930876;DP=434;DP4=0,0,223,206;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 39871.0 PASS AF=0.930736;DP=1155;DP4=0,0,593,559;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 9831.0 PASS AF=0.896667;DP=300;DP4=18,0,118,162;SB=64;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G) NC_045512 20719 . C T 10172.0 PASS AF=0.916944;DP=301;DP4=0,0,186,114;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 21618 . C T 37737.0 PASS AF=0.908015;DP=1098;DP4=0,1,534,546;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 21632 . TTACCCCCTG T 36519.0 PASS AF=0.987215;DP=1095;DP4=19,13,521,560;HRUN=2;SB=5;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 32024.0 PASS AF=0.830606;DP=1039;DP4=6,1,553,478;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22200 . T G 14214.0 PASS AF=0.926014;DP=419;DP4=0,0,178,240;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22578 . G A 31903.0 PASS AF=0.882294;DP=994;DP4=5,2,476,504;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22629 . A C 30661.0 PASS AF=0.921892;DP=909;DP4=0,2,428,478;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 27838.0 PASS AF=0.879490;DP=863;DP4=13,9,365,474;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22674 . C T 24989.0 PASS AF=0.836145;DP=830;DP4=0,5,345,479;SB=10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22679 . T C 27296.0 PASS AF=0.950255;DP=784;DP4=0,0,325,458;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 21778.0 PASS AF=0.854571;DP=722;DP4=1,4,302,413;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22688 . A G 22939.0 PASS AF=0.897250;DP=691;DP4=1,1,295,391;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22716 . C T 19013.0 PASS AF=0.940520;DP=538;DP4=0,0,245,292;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 28337.0 PASS AF=0.840075;DP=1063;DP4=60,70,404,528;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 36993.0 PASS AF=0.908537;DP=1148;DP4=0,1,526,618;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22792 . C T 39448.0 PASS AF=0.923010;DP=1156;DP4=0,0,540,614;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22813 . G T 46605.0 PASS AF=0.910819;DP=1368;DP4=2,2,667,694;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22882 . T G 33218.0 PASS AF=0.903749;DP=987;DP4=3,1,556,426;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22992 . G A 33338.0 PASS AF=0.922686;DP=983;DP4=0,0,439,539;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 35188.0 PASS AF=0.960366;DP=984;DP4=0,0,438,542;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 32197.0 PASS AF=0.884615;DP=988;DP4=3,4,432,546;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 28927.0 PASS AF=0.909817;DP=876;DP4=1,5,392,477;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23055 . A G 25805.0 PASS AF=0.901126;DP=799;DP4=1,0,375,423;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23063 . A T 27086.0 PASS AF=0.935149;DP=771;DP4=1,0,374,395;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 23075 . T C 24760.0 PASS AF=0.923593;DP=746;DP4=1,0,379,366;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 23403 . A G 17764.0 PASS AF=0.926357;DP=516;DP4=0,1,227,287;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 11671.0 PASS AF=0.900285;DP=351;DP4=0,0,169,181;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 23599 . T G 28616.0 PASS AF=0.924641;DP=836;DP4=0,0,423,413;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23604 . C A 27152.0 PASS AF=0.889290;DP=831;DP4=3,0,418,408;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23854 . C A 13443.0 PASS AF=0.882494;DP=417;DP4=0,5,206,205;SB=12;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23948 . G T 19483.0 PASS AF=0.918871;DP=567;DP4=0,0,303,261;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 47157.0 PASS AF=0.917638;DP=1372;DP4=0,10,722,639;SB=32;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=0.940594;DP=1616;DP4=3,0,817,790;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 24966 . A G 37438.0 PASS AF=0.901051;DP=1142;DP4=1,1,515,615;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 25000 . C T 35713.0 PASS AF=0.932551;DP=1023;DP4=0,1,497,520;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 25584 . C T 41364.0 PASS AF=0.868482;DP=1285;DP4=0,2,728,548;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26060 . C T 37722.0 PASS AF=0.959125;DP=1052;DP4=0,0,519,532;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26270 . C T 20075.0 PASS AF=0.910169;DP=590;DP4=2,1,316,270;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512 26577 . C G 28295.0 PASS AF=0.902353;DP=850;DP4=1,0,424,421;SB=0;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=0.932495;DP=1511;DP4=1,0,716,789;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A) NC_045512 26801 . C T 41640.0 PASS AF=0.909458;DP=1237;DP4=0,1,570,663;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 26858 . C T 22508.0 PASS AF=0.874269;DP=684;DP4=0,0,316,365;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 27259 . A C 45374.0 PASS AF=0.890858;DP=1411;DP4=5,10,575,816;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27382 . G C 14766.0 PASS AF=0.901827;DP=438;DP4=1,0,209,227;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 14828.0 PASS AF=0.910138;DP=434;DP4=1,0,207,226;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 14918.0 PASS AF=0.898420;DP=443;DP4=1,0,215,226;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27481 . C T 20803.0 PASS AF=0.941569;DP=599;DP4=0,0,291,304;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) NC_045512 27549 . C T 42020.0 PASS AF=0.897189;DP=1245;DP4=0,0,632,599;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) NC_045512 27807 . C T 17266.0 PASS AF=0.953722;DP=497;DP4=0,0,245,250;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T) NC_045512 28271 . A T 46064.0 PASS AF=0.910096;DP=1357;DP4=2,9,655,689;SB=11 NC_045512 28311 . C T 45477.0 PASS AF=0.818475;DP=1548;DP4=2,13,761,763;SB=21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512 28361 . GGAGAACGCA G 30403.0 PASS AF=0.774089;DP=1235;DP4=184,99,429,527;HRUN=2;SB=85;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 28881 . G A 40833.0 PASS AF=0.945026;DP=1146;DP4=0,0,518,623;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28882 . G A 38295.0 PASS AF=0.908772;DP=1140;DP4=0,1,517,609;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28883 . G C 39272.0 PASS AF=0.923144;DP=1145;DP4=0,0,515,621;SB=0;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=0.924388;DP=2288;DP4=0,1,1031,1246;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 49314.0 PASS AF=0.992537;DP=1340;DP4=133,109,486,844;HRUN=1;SB=69;INDEL