Mercurial > repos > iuc > virheat
view test-data/day_55.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=20220901 ##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/050/129/50129874/tmp/lofreq2_call_parallel_4m1yhf9/0.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_69,Description="Minimum SNV Quality (Phred) 69"> ##FILTER=<ID=min_indelqual_54,Description="Minimum Indel Quality (Phred) 54"> ##FILTER=<ID=min_snvqual_76,Description="Minimum SNV Quality (Phred) 76"> ##FILTER=<ID=min_indelqual_62,Description="Minimum Indel Quality (Phred) 62"> ##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/050/130/50130117/outputs/galaxy_dataset_54d75f13-335c-4bee-9f56-a8cc78951a0e.dat -csvStats /data/jwd01/main/050/130/50130117/outputs/galaxy_dataset_a4477757-f597-48ad-a763-e3d57c7946ec.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/a/9/a/dataset_a9aee115-dacc-4ec4-a915-a667c1f8b549.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 241 . C T 2150.0 PASS AF=0.983607;DP=61;DP4=0,0,30,31;SB=0 NC_045512 509 . GGTCATGTTA G 49314.0 PASS AF=0.990594;DP=2339;DP4=136,167,1257,1060;HRUN=2;SB=26;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 49314.0 PASS AF=0.977359;DP=2915;DP4=0,0,1471,1444;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=0.982265;DP=6428;DP4=27,23,3221,3157;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 1980 . G T 34404.0 PASS AF=0.983871;DP=930;DP4=0,0,458,468;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 49314.0 PASS AF=0.982153;DP=1793;DP4=0,0,892,897;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 49314.0 PASS AF=0.981051;DP=4433;DP4=0,0,2205,2220;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4184 . G A 49314.0 PASS AF=0.988202;DP=2119;DP4=3,2,1183,931;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 49314.0 PASS AF=0.981818;DP=1980;DP4=1,1,1403,575;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 4321 . C T 40010.0 PASS AF=0.657609;DP=1840;DP4=596,8,635,599;SB=1173;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 5628 . C T 49314.0 PASS AF=0.966059;DP=1974;DP4=22,20,938,994;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 6354 . C T 30043.0 PASS AF=0.541788;DP=1711;DP4=774,1,530,406;SB=1263;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 8109 . C T 49314.0 PASS AF=0.968127;DP=2008;DP4=19,16,1017,956;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T2615I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 9344 . C T 49314.0 PASS AF=0.988103;DP=3194;DP4=1,0,1583,1609;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 49314.0 PASS AF=0.976721;DP=3050;DP4=1,1,1520,1528;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=0.987535;DP=5054;DP4=0,0,2472,2582;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 49314.0 PASS AF=0.980011;DP=3652;DP4=5,6,1966,1674;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10029 . C T 49314.0 PASS AF=0.957557;DP=4241;DP4=1,1,2025,2212;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 49314.0 PASS AF=0.984712;DP=2878;DP4=1,1,1450,1423;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 10447 . G A 49314.0 PASS AF=0.981521;DP=1894;DP4=1,1,920,971;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 10449 . C A 49314.0 PASS AF=0.981142;DP=1909;DP4=0,3,934,971;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A) NC_045512 11287 . GTCTGGTTTT G 44284.0 PASS AF=0.994074;DP=1350;DP4=118,131,668,674;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 49314.0 PASS AF=0.977939;DP=3037;DP4=1,0,1500,1533;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T) NC_045512 12854 . C T 49314.0 PASS AF=0.978914;DP=1897;DP4=1,0,953,942;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 49314.0 PASS AF=0.984450;DP=1865;DP4=1,1,927,936;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=0.987194;DP=5232;DP4=2,3,2604,2622;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 49314.0 PASS AF=0.973996;DP=3884;DP4=4,4,2076,1798;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 49314.0 PASS AF=0.982387;DP=2555;DP4=0,1,1249,1301;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T) NC_045512 17410 . C T 49314.0 PASS AF=0.983071;DP=1713;DP4=0,0,872,838;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 49314.0 PASS AF=0.981366;DP=1771;DP4=0,0,876,895;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=0.983919;DP=5410;DP4=0,0,2706,2704;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 49314.0 PASS AF=0.878327;DP=1578;DP4=168,1,696,713;SB=454;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G) NC_045512 20719 . C T 49314.0 PASS AF=0.983268;DP=1793;DP4=1,1,931,860;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=0.992293;DP=4282;DP4=2,3,2045,2232;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 49314.0 PASS AF=0.971920;DP=3490;DP4=211,224,1595,1797;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 49314.0 PASS AF=0.976943;DP=3860;DP4=1,0,2009,1848;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 49314.0 PASS AF=0.978495;DP=2232;DP4=2,3,1064,1163;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 49314.0 PASS AF=0.976501;DP=3830;DP4=2,1,1895,1932;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22629 . A C 49314.0 PASS AF=0.980153;DP=3527;DP4=0,0,1757,1763;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 49314.0 PASS AF=0.977541;DP=3384;DP4=5,4,1661,1711;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 22674 . C T 49314.0 PASS AF=0.974561;DP=3420;DP4=0,1,1667,1752;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 49314.0 PASS AF=0.976274;DP=3414;DP4=2,5,1668,1739;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 22686 . C T 49314.0 PASS AF=0.976059;DP=3258;DP4=4,5,1593,1651;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 49314.0 PASS AF=0.977301;DP=3216;DP4=5,4,1586,1618;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22716 . C T 49314.0 PASS AF=0.985468;DP=3303;DP4=0,1,1676,1625;SB=3;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=0.853479;DP=8579;DP4=496,663,3330,4089;SB=7;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=0.965444;DP=7524;DP4=19,20,3305,4170;SB=2;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=0.983602;DP=7501;DP4=2,1,3333,4164;SB=2;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=0.986985;DP=7914;DP4=0,0,3588,4319;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 49314.0 PASS AF=0.976932;DP=5072;DP4=4,8,2639,2420;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 22992 . G A 49314.0 PASS AF=0.983352;DP=4385;DP4=2,3,2107,2272;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 49314.0 PASS AF=0.985318;DP=4359;DP4=1,0,2105,2251;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A) NC_045512 23013 . A C 49314.0 PASS AF=0.971480;DP=4453;DP4=17,16,2118,2294;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C) NC_045512 23040 . A G 49314.0 PASS AF=0.986637;DP=4490;DP4=0,2,2153,2335;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 49314.0 PASS AF=0.983106;DP=4262;DP4=1,1,2069,2191;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 49314.0 PASS AF=0.992556;DP=4030;DP4=0,0,1975,2053;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 49314.0 PASS AF=0.975079;DP=4093;DP4=2,2,2038,2047;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 32080.0 PASS AF=0.981756;DP=877;DP4=0,0,411,466;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 31898.0 PASS AF=0.982916;DP=878;DP4=1,0,442,434;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=0.984131;DP=3970;DP4=1,1,2073,1895;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 49314.0 PASS AF=0.984480;DP=3866;DP4=0,1,2017,1845;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 49314.0 PASS AF=0.975383;DP=3006;DP4=5,5,1472,1519;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 49314.0 PASS AF=0.978654;DP=3045;DP4=0,0,1551,1490;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=0.984966;DP=6585;DP4=3,3,3360,3219;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=0.981200;DP=7181;DP4=0,0,3618,3562;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 49314.0 PASS AF=0.969872;DP=3983;DP4=3,5,1951,2000;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G) NC_045512 25000 . C T 49314.0 PASS AF=0.982474;DP=3937;DP4=0,2,1940,1995;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T) NC_045512 25584 . C T 49314.0 PASS AF=0.969027;DP=4972;DP4=2,2,2628,2338;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T) NC_045512 26060 . C T 49314.0 PASS AF=0.984340;DP=4917;DP4=3,3,2409,2502;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 49314.0 PASS AF=0.978567;DP=1773;DP4=1,1,889,882;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 49314.0 PASS AF=0.986331;DP=1829;DP4=1,0,942,885;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T) NC_045512 26571 . C T 19089.0 PASS AF=0.257871;DP=2668;DP4=957,1013,332,366;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L17F|222|M|protein_coding|CODING|GU280_gp05|1|T) NC_045512 26577 . C G 49314.0 PASS AF=0.972893;DP=2693;DP4=0,0,1280,1374;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=0.977913;DP=5433;DP4=4,3,2855,2569;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=0.983187;DP=5829;DP4=1,0,2894,2931;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=0.989801;DP=5687;DP4=3,3,2686,2994;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=0.973431;DP=5721;DP4=14,21,2604,3071;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27382 . G C 49314.0 PASS AF=0.987069;DP=1624;DP4=0,0,798,826;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 49314.0 PASS AF=0.974439;DP=1604;DP4=0,0,788,816;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 49314.0 PASS AF=0.985339;DP=1637;DP4=2,0,807,828;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C) NC_045512 27481 . C T 49314.0 PASS AF=0.984321;DP=1722;DP4=0,0,863,858;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 49314.0 PASS AF=0.986065;DP=4234;DP4=1,0,2141,2076;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T) NC_045512 27807 . C T 49314.0 PASS AF=0.985981;DP=2354;DP4=1,1,1167,1184;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=0.985745;DP=7857;DP4=8,11,3861,3975;SB=1 NC_045512 28311 . C T 49314.0 PASS AF=0.957243;DP=7297;DP4=7,4,3570,3710;SB=4;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=0.830892;DP=6280;DP4=717,401,2253,2965;HRUN=2;SB=365;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=0.975592;DP=5531;DP4=3,2,2828,2694;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T) NC_045512 28881 . G A 49314.0 PASS AF=0.977910;DP=2354;DP4=0,0,1161,1193;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 49314.0 PASS AF=0.978916;DP=2324;DP4=0,2,1147,1175;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A) NC_045512 28883 . G C 49314.0 PASS AF=0.981528;DP=2382;DP4=0,0,1174,1207;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=0.977301;DP=7181;DP4=2,2,3340,3833;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=0.991870;DP=2091;DP4=516,513,868,1206;HRUN=1;SB=48;INDEL