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Uploaded results obtained from using this pipeline
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| ##fileformat=VCFv4.2 | ||
| ##FILTER=<ID=PASS,Description="All filters passed"> | ||
| ##bcftoolsVersion=1.13+htslib-1.13+ds | ||
| ##bcftoolsCommand=mpileup -O b -o trim_ERR10000000_sorted.bcf -f /home/focyte/DNA_Variant_Call/data/ref_genome/genome.fasta trim_ERR10000000_sorted.bam | ||
| ##reference=file:///home/focyte/DNA_Variant_Call/data/ref_genome/genome.fasta | ||
| ##contig=<ID=NC_045512.2,length=29903> | ||
| ##ALT=<ID=*,Description="Represents allele(s) other than observed."> | ||
| ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> | ||
| ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel"> | ||
| ##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel"> | ||
| ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> | ||
| ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> | ||
| ##INFO=<ID=RPBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)"> | ||
| ##INFO=<ID=MQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)"> | ||
| ##INFO=<ID=BQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)"> | ||
| ##INFO=<ID=MQSBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)"> | ||
| ##INFO=<ID=SCBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)"> | ||
| ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | ||
| ##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> | ||
| ##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> | ||
| ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> | ||
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
| ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> | ||
| ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> | ||
| ##bcftools_callVersion=1.13+htslib-1.13+ds | ||
| ##bcftools_callCommand=call --ploidy 1 -m -v -o trim_ERR10000000_sorted.vcf trim_ERR10000000_sorted.bcf; Date=Sat Sep 7 20:30:58 2024 | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT trim_ERR10000000_sorted.bam | ||
| NC_045512.2 241 . C T 225.422 . DP=158;VDB=1;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,49,33;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 598 . G A 191.41 . DP=130;VDB=0;SGB=-0.693147;RPBZ=-0.109948;BQBZ=-0.722999;SCBZ=0.652032;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,129;MQ=60 GT:PL 1:218,0 | ||
| NC_045512.2 670 . T G 228.419 . DP=255;VDB=0.99783;SGB=-0.693147;RPBZ=0.274217;MQBZ=6.39041;MQSBZ=-1.12882;BQBZ=5.46834;SCBZ=-3.39264;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,99,153;MQ=59 GT:PL 1:255,0 | ||
| NC_045512.2 2790 . C T 228.396 . DP=283;VDB=0;SGB=-0.693147;RPBZ=7.41811;BQBZ=2.44202;SCBZ=-4.51727;FS=0;MQ0F=0;AC=1;AN=1;DP4=5,2,0,276;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 2954 . T C 99.4152 . DP=5;VDB=0.00231828;SGB=-0.590765;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,0;MQ=60 GT:PL 1:129,0 | ||
| NC_045512.2 3037 . C T 228.429 . DP=265;VDB=0;SGB=-0.693147;RPBZ=3.52425;BQBZ=2.34985;SCBZ=-4.08495;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,264;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 4184 . G A 99.4152 . DP=5;VDB=0.00376034;SGB=-0.590765;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,0;MQ=60 GT:PL 1:129,0 | ||
| NC_045512.2 4321 . C T 162.261 . DP=326;VDB=0;SGB=-0.693147;RPBZ=0.0810705;BQBZ=-1.78162;SCBZ=1.91905;FS=0;MQ0F=0;AC=1;AN=1;DP4=3,20,0,303;MQ=60 GT:PL 1:189,0 | ||
| NC_045512.2 8503 . T C 104.196 . DP=57;VDB=5.92685e-32;SGB=-0.693147;RPBZ=-7.40299;BQBZ=0.740519;FS=0;MQ0F=0;AC=1;AN=1;DP4=6,0,0,50;MQ=60 GT:PL 1:131,0 | ||
| NC_045512.2 9344 . C T 114.415 . DP=7;VDB=8.97585e-05;SGB=-0.636426;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,0;MQ=60 GT:PL 1:144,0 | ||
| NC_045512.2 9424 . A G 225.426 . DP=291;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,291;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 9534 . C T 225.422 . DP=335;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,330;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 10029 . C T 225.422 . DP=245;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,245;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 10198 . C T 137.416 . DP=10;VDB=2.02519e-06;SGB=-0.670168;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,10,0;MQ=60 GT:PL 1:167,0 | ||
| NC_045512.2 10447 . G A 225.422 . DP=345;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,340;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 10449 . C A 228.421 . DP=345;VDB=0;SGB=-0.693147;RPBZ=2.35579;BQBZ=5.12706;SCBZ=-2.94101;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,5,337;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 11750 . C T 37.4152 . DP=2;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,2,0;MQ=60 GT:PL 1:67,0 | ||
| NC_045512.2 12139 . T G 70.0575 . DP=16;VDB=2.26006e-08;SGB=-0.683931;RPBZ=-3.74166;BQBZ=-1.37281;FS=0;MQ0F=0;AC=1;AN=1;DP4=2,0,0,13;MQ=60 GT:PL 1:117,20 | ||
| NC_045512.2 12160 . G A 225.426 . DP=260;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,260;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 12880 . C T 225.417 . DP=280;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,275;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 14408 . C T 225.422 . DP=318;VDB=0;SGB=-0.693147;MQSBZ=-0.12639;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,313;MQ=59 GT:PL 1:255,0 | ||
| NC_045512.2 15714 . C T 225.422 . DP=169;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,169,0;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 16935 . G A 225.426 . DP=259;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,259;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 17410 . C T 137.416 . DP=9;VDB=2.63415e-05;SGB=-0.662043;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,9,0;MQ=60 GT:PL 1:167,0 | ||
| NC_045512.2 18163 . A G 225.422 . DP=272;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,272;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 19955 . C T 152.416 . DP=20;VDB=7.63912e-12;SGB=-0.692067;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,20,0;MQ=60 GT:PL 1:182,0 | ||
| NC_045512.2 20055 . A G 156.421 . DP=20;VDB=1.01052e-12;SGB=-0.692067;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,20;MQ=60 GT:PL 1:186,0 | ||
| NC_045512.2 21618 . C T 225.422 . DP=334;VDB=0;SGB=-0.693147;MQSBZ=-0.0776151;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,2,332;MQ=59 GT:PL 1:255,0 | ||
| NC_045512.2 21987 . G A 99.4152 . DP=5;VDB=0.0041585;SGB=-0.590765;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,0;MQ=60 GT:PL 1:129,0 | ||
| NC_045512.2 22200 . T G 228.421 . DP=335;VDB=0;SGB=-0.693147;RPBZ=2.51766;BQBZ=4.88783;SCBZ=-3.26621;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,3,329;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22578 . G A 12.6615 . DP=3;VDB=0.0249187;SGB=-0.511536;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,0;MQ=60 GT:PL 1:44,2 | ||
| NC_045512.2 22674 . C T 225.417 . DP=217;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,217;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22679 . T C 225.422 . DP=217;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,217;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22686 . C T 225.417 . DP=217;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,217;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22688 . A G 225.422 . DP=217;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,217;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22775 . G A 225.417 . DP=253;VDB=6.91313e-12;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,36,217;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22786 . A C 206.831 . DP=253;VDB=0.0592488;SGB=-0.693147;RPBZ=-2.5404;BQBZ=1.82661;SCBZ=-1.08136;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,67,36,150;MQ=60 GT:PL 1:255,21 | ||
| NC_045512.2 22813 . G T 167.416 . DP=36;VDB=8.04518e-20;SGB=-0.693139;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,36,0;MQ=60 GT:PL 1:197,0 | ||
| NC_045512.2 22882 . T G 169.416 . DP=36;VDB=1.19333e-19;SGB=-0.693139;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,36,0;MQ=60 GT:PL 1:199,0 | ||
| NC_045512.2 22917 . T G 225.417 . DP=39;VDB=9.68749e-07;SGB=-0.693144;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,36,3;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22992 . G A 225.422 . DP=239;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,174,62;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 22995 . C A 228.382 . DP=239;VDB=0;SGB=-0.693147;RPBZ=2.5113;BQBZ=6.95375;SCBZ=-8.60039;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,10,174,52;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23013 . A C 228.418 . DP=242;VDB=0;SGB=-0.693147;RPBZ=0.347064;BQBZ=-0.323676;SCBZ=0.33876;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,0,173,68;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23018 . T G 228.421 . DP=243;VDB=0;SGB=-0.693147;RPBZ=2.00708;BQBZ=3.30828;SCBZ=-3.2151;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,174,68;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23055 . A G 225.422 . DP=253;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,174,79;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23063 . A T 225.422 . DP=254;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,174,80;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23075 . T C 225.422 . DP=255;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,174,81;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23403 . A G 225.417 . DP=43;VDB=0.999997;SGB=-0.693146;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,17,26;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23525 . C T 225.426 . DP=287;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,287;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23599 . T G 228.419 . DP=324;VDB=0;SGB=-0.693147;RPBZ=-0.840222;BQBZ=5.25537;SCBZ=0.99831;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,4,2,318;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23604 . C A 225.422 . DP=324;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,2,322;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23854 . C A 228.414 . DP=287;VDB=0;SGB=-0.693147;RPBZ=4.23486;BQBZ=6.42322;SCBZ=-2.66166;FS=0;MQ0F=0;AC=1;AN=1;DP4=2,2,0,283;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 23948 . G T 62.4147 . DP=3;VDB=0.0249187;SGB=-0.511536;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,0;MQ=60 GT:PL 1:92,0 | ||
| NC_045512.2 24424 . A T 228.426 . DP=279;VDB=0;SGB=-0.693147;RPBZ=3.7095;BQBZ=3.79321;SCBZ=-5.75086;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,4,0,275;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 24469 . T A 228.426 . DP=287;VDB=0;SGB=-0.693147;RPBZ=1.9025;BQBZ=2.67402;SCBZ=-2.66377;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,5,280;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 25000 . C T 225.422 . DP=267;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,267;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 25584 . C T 225.426 . DP=264;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,264;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 26060 . C T 225.422 . DP=252;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,252,0;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 26270 . C T 225.426 . DP=255;VDB=2.68816e-21;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,182,73;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 26529 . G A 228.426 . DP=223;VDB=0;SGB=-0.693147;RPBZ=0.205055;BQBZ=-0.553403;SCBZ=0.584115;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,222;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 26577 . C G 228.429 . DP=241;VDB=0;SGB=-0.693147;RPBZ=1.78977;BQBZ=2.38411;SCBZ=-1.95599;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,240;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 26709 . G A 110.415 . DP=7;VDB=0.000116031;SGB=-0.636426;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,0;MQ=60 GT:PL 1:140,0 | ||
| NC_045512.2 27807 . C T 225.417 . DP=286;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,283;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 27889 . C T 44.4146 . DP=3;VDB=0.0249187;SGB=-0.511536;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,0;MQ=60 GT:PL 1:74,0 | ||
| NC_045512.2 27904 . T G 96.1873 . DP=31;VDB=1.30483e-15;SGB=-0.693021;RPBZ=-5.37853;BQBZ=-0.738549;FS=0;MQ0F=0;AC=1;AN=1;DP4=3,0,0,27;MQ=60 GT:PL 1:123,0 | ||
| NC_045512.2 28271 . A T 228.427 . DP=297;VDB=0;SGB=-0.693147;RPBZ=4.47295;BQBZ=5.47785;SCBZ=-3.79259;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,4,249,44;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 28311 . C T 225.426 . DP=316;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,249,67;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 28370 . A T 4.38466 . DP=5;VDB=0.0058656;SGB=-0.556411;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,4,0;MQ=60 GT:PL 1:32,0 | ||
| NC_045512.2 28681 . G T 228.405 . DP=251;VDB=0;SGB=-0.693147;RPBZ=0.292245;BQBZ=4.23819;SCBZ=0.157135;FS=0;MQ0F=0;AC=1;AN=1;DP4=6,0,242,1;MQ=60 GT:PL 1:255,0 | ||
| NC_045512.2 28881 . G A 225.426 . DP=291;VDB=0;SGB=-0.693147;MQSBZ=-0.205185;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,4,287;MQ=59 GT:PL 1:255,0 | ||
| NC_045512.2 28882 . G A 225.426 . DP=291;VDB=0;SGB=-0.693147;MQSBZ=-0.205185;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,4,287;MQ=59 GT:PL 1:255,0 | ||
| NC_045512.2 28883 . G C 225.422 . DP=291;VDB=0;SGB=-0.693147;MQSBZ=-0.205185;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,4,287;MQ=59 GT:PL 1:255,0 | ||
| NC_045512.2 29510 . A C 228.426 . DP=325;VDB=0;SGB=-0.693147;RPBZ=1.75653;BQBZ=5.26859;SCBZ=-2.14296;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,6,316;MQ=60 GT:PL 1:255,0 |
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