Mercurial > repos > iuc > virheat
diff test-data/day_18.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 | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/day_18.vcf Wed May 15 13:37:49 2024 +0000 @@ -0,0 +1,113 @@ +##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/jwd/main/050/063/50063644/tmp/lofreq2_call_parallel717nv31u/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_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/jwd/main/050/063/50063750/outputs/galaxy_dataset_232ae126-f2f4-472c-bf70-443ea6a4b576.dat -csvStats /data/jwd/main/050/063/50063750/outputs/galaxy_dataset_801f99b1-8ef7-4504-b4e3-a04f423e6349.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/a/3/d/dataset_a3de6b1f-173b-4ce7-85a4-51a14281eafa.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 26636.0 PASS AF=0.998797;DP=831;DP4=20,27,616,214;HRUN=2;SB=49;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 18624.0 PASS AF=0.951128;DP=532;DP4=0,0,250,281;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=0.969347;DP=1990;DP4=1,0,1026,960;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 4529.0 PASS AF=0.967742;DP=124;DP4=0,0,67,57;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 8006.0 PASS AF=0.969163;DP=227;DP4=0,0,116,111;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 28216.0 PASS AF=0.962963;DP=783;DP4=0,1,361,419;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) +NC_045512 4184 . G A 9244.0 PASS AF=0.968627;DP=255;DP4=0,0,174,81;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 7858.0 PASS AF=0.981132;DP=212;DP4=0,0,173,39;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) +NC_045512 4321 . C T 1600.0 PASS AF=0.460870;DP=115;DP4=61,0,27,27;SB=108;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) +NC_045512 6354 . C T 4133.0 PASS AF=0.774834;DP=151;DP4=29,1,80,41;SB=33;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) +NC_045512 9344 . C T 23951.0 PASS AF=0.977169;DP=657;DP4=1,0,317,339;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) +NC_045512 9424 . A G 21689.0 PASS AF=0.959217;DP=613;DP4=0,0,318,294;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) +NC_045512 9534 . C T 49314.0 PASS AF=0.974796;DP=1349;DP4=0,0,545,804;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 23400.0 PASS AF=0.959815;DP=647;DP4=0,0,481,166;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 23958.0 PASS AF=0.933430;DP=691;DP4=0,0,283,405;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 17239.0 PASS AF=0.942623;DP=488;DP4=0,0,252,235;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) +NC_045512 10447 . G A 12177.0 PASS AF=0.942197;DP=346;DP4=0,1,178,167;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) +NC_045512 10449 . C A 11904.0 PASS AF=0.924638;DP=345;DP4=0,1,177,166;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) +NC_045512 11287 . GTCTGGTTTT G 3147.0 PASS AF=1.000000;DP=96;DP4=5,12,39,57;HRUN=1;SB=3;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G) +NC_045512 12036 . C T 19886.0 PASS AF=0.951473;DP=577;DP4=0,1,262,313;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 13932.0 PASS AF=0.968750;DP=384;DP4=1,1,181,201;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 13710.0 PASS AF=0.973545;DP=378;DP4=0,0,171,207;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=0.966997;DP=1515;DP4=0,0,790,723;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 36998.0 PASS AF=0.948989;DP=1039;DP4=0,0,768,270;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 23967.0 PASS AF=0.978626;DP=655;DP4=0,0,327,328;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) +NC_045512 17259 . G T 671.0 PASS AF=0.217742;DP=124;DP4=51,45,25,3;SB=34;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaT|E5670D|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) +NC_045512 17410 . C T 3135.0 PASS AF=0.977273;DP=88;DP4=0,0,39,49;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 6626.0 PASS AF=0.978261;DP=184;DP4=0,0,87,97;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 48074.0 PASS AF=0.976209;DP=1303;DP4=0,0,917,385;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 13443.0 PASS AF=0.938303;DP=389;DP4=14,1,179,195;SB=34;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G) +NC_045512 20719 . C T 15386.0 PASS AF=0.965035;DP=429;DP4=0,0,235,194;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) +NC_045512 21618 . C T 49314.0 PASS AF=0.987821;DP=1478;DP4=1,0,719,758;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512 21632 . TTACCCCCTG T 47313.0 PASS AF=0.994092;DP=1354;DP4=32,30,649,697;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 21987 . G A 34703.0 PASS AF=0.945697;DP=976;DP4=2,1,451,520;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512 22200 . T G 6387.0 PASS AF=0.967742;DP=186;DP4=0,0,93,93;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 21408.0 PASS AF=0.965347;DP=606;DP4=0,0,314,291;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512 22629 . A C 19252.0 PASS AF=0.964750;DP=539;DP4=1,1,290,247;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 19308.0 PASS AF=0.977570;DP=535;DP4=0,0,277,256;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 18944.0 PASS AF=0.964618;DP=537;DP4=0,0,282,255;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 18999.0 PASS AF=0.964684;DP=538;DP4=0,0,287,251;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 17680.0 PASS AF=0.964497;DP=507;DP4=1,0,271,235;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 17586.0 PASS AF=0.950000;DP=500;DP4=1,0,268,228;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 19310.0 PASS AF=0.967985;DP=531;DP4=0,0,297,234;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=0.881262;DP=2535;DP4=102,110,1368,953;SB=25;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=0.941202;DP=2347;DP4=0,1,1367,974;SB=3;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=0.966311;DP=2345;DP4=1,1,1366,976;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=0.969281;DP=2474;DP4=0,1,1430,1042;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512 22882 . T G 49314.0 PASS AF=0.958710;DP=1768;DP4=2,1,1209,555;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 36772.0 PASS AF=0.964355;DP=1038;DP4=0,0,475,563;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 37275.0 PASS AF=0.970760;DP=1026;DP4=0,0,471,555;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 36561.0 PASS AF=0.965174;DP=1005;DP4=2,0,456,545;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C) +NC_045512 23040 . A G 34886.0 PASS AF=0.978079;DP=958;DP4=0,1,442,515;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 33387.0 PASS AF=0.962065;DP=949;DP4=0,1,448,500;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 33872.0 PASS AF=0.985792;DP=915;DP4=0,0,449,464;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 31911.0 PASS AF=0.961538;DP=910;DP4=0,0,458,452;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 12029.0 PASS AF=0.972973;DP=333;DP4=0,0,161,172;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 11185.0 PASS AF=0.973941;DP=307;DP4=0,0,164,143;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 49314.0 PASS AF=0.958807;DP=1408;DP4=0,1,739,667;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 49314.0 PASS AF=0.968750;DP=1408;DP4=0,0,740,668;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512 23854 . C A 18583.0 PASS AF=0.942379;DP=538;DP4=1,2,258,276;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 21728.0 PASS AF=0.959933;DP=599;DP4=0,0,306,293;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 49314.0 PASS AF=0.950000;DP=2320;DP4=1,1,1222,1094;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=0.951425;DP=2491;DP4=1,1,1302,1183;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A) +NC_045512 24966 . A G 31324.0 PASS AF=0.953933;DP=890;DP4=0,0,408,477;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 30573.0 PASS AF=0.961131;DP=849;DP4=1,0,382,463;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T) +NC_045512 25584 . C T 41217.0 PASS AF=0.963781;DP=1132;DP4=1,3,726,402;SB=8;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) +NC_045512 26060 . C T 41883.0 PASS AF=0.971706;DP=1131;DP4=0,0,506,622;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 7270.0 PASS AF=0.980099;DP=201;DP4=0,0,92,109;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 6219.0 PASS AF=0.970930;DP=172;DP4=0,0,95,77;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 19291.0 PASS AF=0.961039;DP=539;DP4=0,0,247,292;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 49071.0 PASS AF=0.968148;DP=1350;DP4=1,1,848,498;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=0.961560;DP=1795;DP4=0,0,913,881;SB=0;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=0.979244;DP=1349;DP4=0,0,509,839;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=0.973325;DP=1537;DP4=1,1,428,1105;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) +NC_045512 27382 . G C 7064.0 PASS AF=0.954082;DP=196;DP4=0,0,95,101;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 7052.0 PASS AF=0.958549;DP=193;DP4=0,0,94,99;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 7096.0 PASS AF=0.953846;DP=195;DP4=1,1,94,99;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) +NC_045512 27481 . C T 10114.0 PASS AF=0.971530;DP=281;DP4=0,0,151,130;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 38892.0 PASS AF=0.978988;DP=1047;DP4=0,0,543,504;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) +NC_045512 27807 . C T 10876.0 PASS AF=0.967427;DP=307;DP4=1,0,152,154;SB=3;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=0.971286;DP=2403;DP4=1,1,1260,1141;SB=0 +NC_045512 28311 . C T 49314.0 PASS AF=0.913405;DP=2402;DP4=2,4,1245,1144;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 49314.0 PASS AF=0.682846;DP=2122;DP4=617,58,445,1004;HRUN=2;SB=1661;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 49314.0 PASS AF=0.943368;DP=2013;DP4=1,0,996,1013;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T) +NC_045512 28881 . G A 20426.0 PASS AF=0.958929;DP=560;DP4=1,0,283,276;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 19564.0 PASS AF=0.928571;DP=560;DP4=0,0,284,274;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) +NC_045512 28883 . G C 20254.0 PASS AF=0.952297;DP=566;DP4=0,0,285,280;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=0.958883;DP=1970;DP4=0,2,778,1187;SB=2;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=0.995888;DP=1216;DP4=89,86,224,987;HRUN=1;SB=180;INDEL