Mercurial > repos > iuc > virheat
view test-data/day_32.vcf @ 3:b5411b5e8259 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
| author | iuc |
|---|---|
| date | Mon, 26 Aug 2024 18:10:25 +0000 |
| parents | d2a1ac520392 |
| children |
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##fileformat=VCFv4.0 ##fileDate=20220830 ##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/050/067/50067391/tmp/lofreq2_call_parallel84g9etws/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_63,Description="Minimum SNV Quality (Phred) 63"> ##FILTER=<ID=min_indelqual_48,Description="Minimum Indel Quality (Phred) 48"> ##FILTER=<ID=min_snvqual_71,Description="Minimum SNV Quality (Phred) 71"> ##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57"> ##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/050/067/50067628/outputs/galaxy_dataset_776fff03-e254-4dfb-abbf-8d93b9cfb46b.dat -csvStats /data/jwd01/main/050/067/50067628/outputs/galaxy_dataset_fb58a8b5-8934-4d3e-9ea4-2b45f3933814.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/7/6/b/dataset_76b4f78f-44ca-48ff-9ffb-46fda2231d70.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 15763.0 PASS AF=0.991903;DP=494;DP4=25,25,293,197;HRUN=2;SB=6;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 19515.0 PASS AF=0.969369;DP=555;DP4=0,0,280,275;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 38595.0 PASS AF=0.975285;DP=1052;DP4=5,2,514,531;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 1980 . G T 10895.0 PASS AF=0.966443;DP=298;DP4=0,0,153,144;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 15238.0 PASS AF=0.966903;DP=423;DP4=0,0,204,219;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 26967.0 PASS AF=0.966533;DP=747;DP4=0,0,361,383;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4184 . G A 10051.0 PASS AF=0.978102;DP=274;DP4=0,0,162,112;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 10845.0 PASS AF=0.983051;DP=295;DP4=0,0,216,79;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4321 . C T 6431.0 PASS AF=0.716475;DP=261;DP4=65,3,103,90;SB=108;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 5628 . C T 3005.0 PASS AF=0.293011;DP=372;DP4=113,147,57,54;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 6354 . C T 7773.0 PASS AF=0.760274;DP=292;DP4=66,1,132,93;SB=113;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9344 . C T 20585.0 PASS AF=0.982206;DP=562;DP4=0,0,283,279;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 18743.0 PASS AF=0.965779;DP=526;DP4=2,2,253,268;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 9534 . C T 34480.0 PASS AF=0.985808;DP=916;DP4=0,1,445,469;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 19606.0 PASS AF=0.983114;DP=533;DP4=0,0,315,218;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 23751.0 PASS AF=0.944035;DP=679;DP4=0,1,306,372;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 19726.0 PASS AF=0.990637;DP=534;DP4=0,0,281,253;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10447 . G A 11857.0 PASS AF=0.951662;DP=331;DP4=0,0,164,165;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 10449 . C A 11818.0 PASS AF=0.954407;DP=329;DP4=0,1,164,163;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 11287 . GTCTGGTTTT G 6182.0 PASS AF=0.994872;DP=195;DP4=21,21,89,105;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) NC_045512 12036 . C T 18290.0 PASS AF=0.963178;DP=516;DP4=0,0,258,258;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 14548.0 PASS AF=0.967172;DP=396;DP4=1,2,200,193;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 12880 . C T 14683.0 PASS AF=0.984810;DP=395;DP4=0,0,197,198;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 14408 . C T 39342.0 PASS AF=0.971216;DP=1077;DP4=1,2,531,543;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 15451 . G A 26255.0 PASS AF=0.969655;DP=725;DP4=0,0,411,313;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 21454.0 PASS AF=0.972789;DP=588;DP4=0,0,282,306;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 17410 . C T 9474.0 PASS AF=0.984496;DP=258;DP4=0,0,127,131;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 12021.0 PASS AF=0.970326;DP=337;DP4=0,0,168,169;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 28596.0 PASS AF=0.973180;DP=783;DP4=0,0,463,318;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 11442.0 PASS AF=0.968051;DP=313;DP4=0,0,156,157;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G) NC_045512 20719 . C T 15802.0 PASS AF=0.976798;DP=431;DP4=0,0,237,194;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 21618 . C T 40675.0 PASS AF=0.983441;DP=1087;DP4=1,2,533,551;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 32959.0 PASS AF=0.983211;DP=953;DP4=39,46,461,476;HRUN=2;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 21691 . C T 4169.0 PASS AF=0.155660;DP=1060;DP4=430,461,81,88;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F43|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 21987 . G A 29742.0 PASS AF=0.954816;DP=841;DP4=1,0,431,407;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22200 . T G 14370.0 PASS AF=0.973105;DP=409;DP4=0,0,199,210;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 21245.0 PASS AF=0.974790;DP=595;DP4=1,0,296,298;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22629 . A C 19866.0 PASS AF=0.971377;DP=559;DP4=0,0,284,275;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22664 . C A 20854.0 PASS AF=0.972028;DP=572;DP4=0,0,277,292;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 20794.0 PASS AF=0.974315;DP=584;DP4=0,0,280,303;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 20993.0 PASS AF=0.976190;DP=588;DP4=0,0,286,302;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 19322.0 PASS AF=0.967332;DP=551;DP4=0,1,267,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 22688 . A G 19389.0 PASS AF=0.970588;DP=544;DP4=0,0,267,276;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 20710.0 PASS AF=0.989267;DP=559;DP4=0,0,282,277;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 42814.0 PASS AF=0.980375;DP=1172;DP4=2,6,574,590;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22786 . A C 43361.0 PASS AF=0.963816;DP=1216;DP4=0,0,597,619;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 46048.0 PASS AF=0.977689;DP=1255;DP4=0,0,614,641;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=0.978801;DP=1368;DP4=0,0,679,686;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 38759.0 PASS AF=0.966102;DP=1062;DP4=1,0,595,466;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22992 . G A 30675.0 PASS AF=0.978873;DP=852;DP4=0,0,387,464;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 30708.0 PASS AF=0.978495;DP=837;DP4=0,0,384,453;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 30583.0 PASS AF=0.974760;DP=832;DP4=0,0,377,454;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 29750.0 PASS AF=0.985240;DP=813;DP4=0,0,371,442;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23055 . A G 28119.0 PASS AF=0.969620;DP=790;DP4=1,2,367,420;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 27561.0 PASS AF=0.990553;DP=741;DP4=0,0,359,382;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 26731.0 PASS AF=0.960681;DP=763;DP4=2,2,379,380;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 14034.0 PASS AF=0.966752;DP=391;DP4=0,0,179,212;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 14033.0 PASS AF=0.981771;DP=384;DP4=0,0,204,180;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 23589 . C A 5160.0 PASS AF=0.188293;DP=1025;DP4=439,391,104,90;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T676N|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23599 . T G 38164.0 PASS AF=0.969466;DP=1048;DP4=0,1,549,497;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 23604 . C A 38022.0 PASS AF=0.982592;DP=1034;DP4=0,1,541,490;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23854 . C A 21304.0 PASS AF=0.960000;DP=600;DP4=0,1,283,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23948 . G T 22285.0 PASS AF=0.971901;DP=605;DP4=0,0,315,290;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 48760.0 PASS AF=0.975392;DP=1341;DP4=1,1,682,657;SB=0;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=0.966245;DP=1422;DP4=0,2,719,698;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 30117.0 PASS AF=0.970203;DP=839;DP4=0,0,399,437;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 32463.0 PASS AF=0.964126;DP=892;DP4=0,1,436,454;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 25584 . C T 37535.0 PASS AF=0.959499;DP=1037;DP4=0,1,579,457;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26060 . C T 43542.0 PASS AF=0.979644;DP=1179;DP4=0,0,582,596;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26195 . C T 18449.0 PASS AF=0.959770;DP=522;DP4=1,0,262,258;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 20039.0 PASS AF=0.965704;DP=554;DP4=2,3,280,269;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512 26408 . C T 24554.0 PASS AF=0.633469;DP=1225;DP4=225,182,408,383;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512 26577 . C G 24616.0 PASS AF=0.974889;DP=677;DP4=2,1,309,364;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G) NC_045512 26709 . G A 47953.0 PASS AF=0.966641;DP=1319;DP4=0,0,741,577;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 49314.0 PASS AF=0.973983;DP=1499;DP4=0,1,758,740;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 26858 . C T 49314.0 PASS AF=0.988078;DP=1342;DP4=0,0,605,737;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 27259 . A C 47693.0 PASS AF=0.965004;DP=1343;DP4=3,5,560,770;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27382 . G C 14516.0 PASS AF=0.971795;DP=390;DP4=0,0,187,201;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27383 . A T 14641.0 PASS AF=0.981959;DP=388;DP4=0,0,187,201;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T) NC_045512 27384 . T C 14550.0 PASS AF=0.972010;DP=393;DP4=0,0,189,202;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27481 . C T 16357.0 PASS AF=0.977728;DP=449;DP4=0,0,230,219;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 36762.0 PASS AF=0.980080;DP=1004;DP4=1,0,512,489;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) NC_045512 27807 . C T 22385.0 PASS AF=0.978723;DP=611;DP4=1,1,311,298;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=0.973483;DP=1697;DP4=0,1,853,843;SB=3 NC_045512 28311 . C T 49314.0 PASS AF=0.939506;DP=1620;DP4=0,2,794,819;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512 28361 . GGAGAACGCA G 37520.0 PASS AF=0.786337;DP=1376;DP4=247,53,394,688;HRUN=2;SB=465;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 28657 . C T 45171.0 PASS AF=0.964511;DP=1268;DP4=1,1,668,597;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512 28881 . G A 20403.0 PASS AF=0.960714;DP=560;DP4=1,1,271,287;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 19828.0 PASS AF=0.942755;DP=559;DP4=0,0,271,287;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28883 . G C 20716.0 PASS AF=0.970280;DP=572;DP4=0,0,277,295;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=0.966520;DP=1822;DP4=0,0,792,1028;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 21485.0 PASS AF=0.981550;DP=542;DP4=94,101,189,343;HRUN=1;SB=25;INDEL