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trim_ERR10000288_sorted.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##bcftoolsVersion=1.13+htslib-1.13+ds
##bcftoolsCommand=mpileup -O b -o trim_ERR10000288_sorted.bcf -f /home/focyte/DNA_Variant_Call/data/ref_genome/genome.fasta trim_ERR10000288_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_ERR10000288_sorted.vcf trim_ERR10000288_sorted.bcf; Date=Sat Sep 7 20:34:12 2024
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT trim_ERR10000288_sorted.bam
NC_045512.2 670 . T G 225.422 . DP=256;VDB=0.00058757;SGB=-0.693147;MQSBZ=-2.9503;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,190,66;MQ=59 GT:PL 1:255,0
NC_045512.2 1627 . C T 228.401 . DP=250;VDB=0;SGB=-0.693147;RPBZ=0.181788;BQBZ=-0.295136;SCBZ=0.110208;FS=0;MQ0F=0;AC=1;AN=1;DP4=3,0,247,0;MQ=60 GT:PL 1:255,0
NC_045512.2 2790 . C T 228.355 . DP=263;VDB=0;SGB=-0.693147;RPBZ=10.9258;BQBZ=2.88544;SCBZ=-9.3537;FS=0;MQ0F=0;AC=1;AN=1;DP4=8,2,0,253;MQ=60 GT:PL 1:255,0
NC_045512.2 3037 . C T 228.429 . DP=263;VDB=0;SGB=-0.693147;RPBZ=2.57446;BQBZ=1.91199;SCBZ=-3.59501;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,262;MQ=60 GT:PL 1:255,0
NC_045512.2 3594 . T G 8.72598 . DP=250;VDB=0;SGB=-0.693147;RPBZ=-15.2019;BQBZ=-1.8551;FS=0;MQ0F=0;AC=1;AN=1;DP4=7,27,0,214;MQ=60 GT:PL 1:35,0
NC_045512.2 4184 . G A 104.415 . DP=7;VDB=0.01488;SGB=-0.636426;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,0;MQ=60 GT:PL 1:134,0
NC_045512.2 4321 . C T 184.332 . DP=300;VDB=0;SGB=-0.693147;RPBZ=3.48589;BQBZ=-1.6248;SCBZ=0.67695;FS=0;MQ0F=0;AC=1;AN=1;DP4=4,8,0,287;MQ=60 GT:PL 1:211,0
NC_045512.2 6478 . T G 5.19624 . DP=3;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,0,2,0;MQ=60 GT:PL 1:59,28
NC_045512.2 9344 . C T 225.417 . DP=238;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,237,1;MQ=60 GT:PL 1:255,0
NC_045512.2 9424 . A G 167.426 . DP=66;VDB=1.19792e-20;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,66;MQ=59 GT:PL 1:197,0
NC_045512.2 9534 . C T 225.417 . DP=254;VDB=0.697408;SGB=-0.693147;MQSBZ=-1.84871;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,160,94;MQ=59 GT:PL 1:255,0
NC_045512.2 10029 . C T 225.417 . DP=159;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,159;MQ=60 GT:PL 1:255,0
NC_045512.2 10198 . C T 196.416 . DP=85;VDB=3.54529e-43;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,85,0;MQ=60 GT:PL 1:226,0
NC_045512.2 10447 . G A 225.426 . DP=269;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,262;MQ=60 GT:PL 1:255,0
NC_045512.2 10449 . C A 228.42 . DP=296;VDB=0;SGB=-0.693147;RPBZ=1.51807;BQBZ=3.69148;SCBZ=-2.12818;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,7,287;MQ=60 GT:PL 1:255,0
NC_045512.2 11296 . T G 130.22 . DP=23;VDB=2.77121e-11;SGB=-0.69168;RPBZ=2.97688;BQBZ=3.32128;SCBZ=-3.95059;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,4,0,19;MQ=60 GT:PL 1:157,0
NC_045512.2 12160 . G A 225.422 . DP=256;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,255;MQ=60 GT:PL 1:255,0
NC_045512.2 12880 . C T 225.426 . DP=285;VDB=0;SGB=-0.693147;MQSBZ=-0.158682;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,278;MQ=59 GT:PL 1:255,0
NC_045512.2 14408 . C T 225.417 . DP=272;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,10,262;MQ=60 GT:PL 1:255,0
NC_045512.2 15714 . C T 180.416 . DP=9;VDB=0.992015;SGB=-0.662043;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,3;MQ=60 GT:PL 1:210,0
NC_045512.2 17410 . C T 125.416 . DP=8;VDB=0.0115093;SGB=-0.651104;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,8,0;MQ=60 GT:PL 1:155,0
NC_045512.2 18163 . A G 225.426 . DP=275;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,1,274;MQ=60 GT:PL 1:255,0
NC_045512.2 19955 . C 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 20055 . A G 225.426 . DP=267;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,265;MQ=60 GT:PL 1:255,0
NC_045512.2 21618 . C T 225.422 . DP=280;VDB=0;SGB=-0.693147;MQSBZ=-0.171815;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,8,271;MQ=59 GT:PL 1:255,0
NC_045512.2 21764 . ATACATGTCT ATCT 228.429 . INDEL;IDV=236;IMF=0.971193;DP=243;VDB=0;SGB=-0.693147;RPBZ=-1.88638;SCBZ=-5.8064;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,0,236;MQ=60 GT:PL 1:255,0
NC_045512.2 21987 . G A 132.416 . DP=8;VDB=1.82474e-05;SGB=-0.651104;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,8,0;MQ=60 GT:PL 1:162,0
NC_045512.2 22200 . T G 225.417 . DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,243;MQ=60 GT:PL 1:255,0
NC_045512.2 22775 . G A 225.417 . DP=255;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,255,0;MQ=60 GT:PL 1:255,0
NC_045512.2 22786 . A C 225.417 . DP=255;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,255,0;MQ=60 GT:PL 1:255,0
NC_045512.2 22813 . G T 225.417 . DP=255;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,255,0;MQ=60 GT:PL 1:255,0
NC_045512.2 22882 . T G 228.422 . DP=256;VDB=0;SGB=-0.693147;RPBZ=-0.243328;BQBZ=4.26133;SCBZ=0.0887356;FS=0;MQ0F=0;AC=1;AN=1;DP4=2,0,253,1;MQ=60 GT:PL 1:255,0
NC_045512.2 22917 . T G 225.422 . DP=256;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,255,1;MQ=60 GT:PL 1:255,0
NC_045512.2 22992 . G A 225.417 . DP=58;VDB=1.25927e-34;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,52;MQ=60 GT:PL 1:255,0
NC_045512.2 22995 . C A 228.368 . DP=58;VDB=2.17624e-35;SGB=-0.693147;RPBZ=0.644934;BQBZ=1.26796;SCBZ=-0.750685;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,6,50;MQ=60 GT:PL 1:255,0
NC_045512.2 23013 . A C 228.425 . DP=64;VDB=4.84769e-31;SGB=-0.693147;RPBZ=-0.218061;BQBZ=1.99345;SCBZ=0.599333;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,6,57;MQ=60 GT:PL 1:255,0
NC_045512.2 23018 . T G 228.333 . DP=67;VDB=3.11952e-31;SGB=-0.693147;RPBZ=1.69354;BQBZ=3.96423;SCBZ=-1.53587;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,6,6,55;MQ=60 GT:PL 1:255,0
NC_045512.2 23055 . A G 225.417 . DP=85;VDB=1.16653e-16;SGB=-0.693147;MQSBZ=-0.275589;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,79;MQ=59 GT:PL 1:255,0
NC_045512.2 23063 . A T 225.426 . DP=85;VDB=6.05403e-19;SGB=-0.693147;MQSBZ=-0.275589;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,79;MQ=59 GT:PL 1:255,0
NC_045512.2 23075 . T C 225.422 . DP=87;VDB=1.10622e-19;SGB=-0.693147;MQSBZ=-0.272166;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,81;MQ=59 GT:PL 1:255,0
NC_045512.2 23403 . A G 225.417 . DP=43;VDB=0.869637;SGB=-0.693144;MQSBZ=-0.974679;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,32;MQ=58 GT:PL 1:255,0
NC_045512.2 23525 . C T 228.427 . DP=271;VDB=0;SGB=-0.693147;RPBZ=0.27956;MQBZ=-0.122168;MQSBZ=-0.0862255;BQBZ=4.35669;SCBZ=-1.48449;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,1,268;MQ=59 GT:PL 1:255,0
NC_045512.2 23599 . T G 228.423 . DP=312;VDB=0;SGB=-0.693147;RPBZ=-0.406003;MQBZ=8.73222;MQSBZ=-0.198348;BQBZ=4.40736;SCBZ=-1.11666;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,6,304;MQ=59 GT:PL 1:255,0
NC_045512.2 23604 . C A 228.427 . DP=314;VDB=0;SGB=-0.693147;RPBZ=2.61754;MQBZ=-0.113591;MQSBZ=-0.198023;BQBZ=3.90661;SCBZ=-3.15003;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,6,305;MQ=59 GT:PL 1:255,0
NC_045512.2 23854 . C A 228.425 . DP=280;VDB=0;SGB=-0.693147;RPBZ=2.33587;BQBZ=2.74289;SCBZ=0.312661;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,0,0,279;MQ=60 GT:PL 1:255,0
NC_045512.2 23948 . G T 88.415 . DP=4;VDB=0.0257451;SGB=-0.556411;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,1;MQ=60 GT:PL 1:118,0
NC_045512.2 24424 . A T 228.427 . DP=270;VDB=0;SGB=-0.693147;RPBZ=0.272859;BQBZ=-0.574231;SCBZ=0.3119;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,269;MQ=60 GT:PL 1:255,0
NC_045512.2 24469 . T A 225.422 . DP=283;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,8,275;MQ=60 GT:PL 1:255,0
NC_045512.2 25000 . C T 225.422 . DP=265;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,265;MQ=60 GT:PL 1:255,0
NC_045512.2 25584 . C T 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 26060 . C T 121.415 . DP=8;VDB=1.82474e-05;SGB=-0.651104;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,8,0;MQ=60 GT:PL 1:151,0
NC_045512.2 26177 . C T 225.417 . DP=251;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,251;MQ=60 GT:PL 1:255,0
NC_045512.2 26270 . C T 228.419 . DP=289;VDB=0;SGB=-0.693147;RPBZ=1.71434;BQBZ=-0.539821;SCBZ=-2.87312;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,7,281;MQ=60 GT:PL 1:255,0
NC_045512.2 26529 . G A 225.422 . DP=275;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,273;MQ=60 GT:PL 1:255,0
NC_045512.2 26577 . C G 228.429 . DP=284;VDB=0;SGB=-0.693147;RPBZ=2.19786;BQBZ=2.82916;SCBZ=-2.82816;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,274;MQ=60 GT:PL 1:255,0
NC_045512.2 26709 . G A 119.415 . DP=7;VDB=0.000207967;SGB=-0.636426;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,0;MQ=60 GT:PL 1:149,0
NC_045512.2 27038 . A G 225.417 . DP=15;VDB=0.99758;SGB=-0.680642;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,6;MQ=60 GT:PL 1:255,0
NC_045512.2 27807 . C T 225.417 . DP=292;VDB=0;SGB=-0.693147;MQSBZ=-0.144841;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,286;MQ=59 GT:PL 1:255,0
NC_045512.2 27889 . C T 150.416 . DP=8;VDB=0.422204;SGB=-0.636426;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,1;MQ=60 GT:PL 1:180,0
NC_045512.2 27904 . T G 46.0709 . DP=46;VDB=3.75937e-20;SGB=-0.693144;RPBZ=-6.67954;BQBZ=-0.642191;SCBZ=-2.36039;FS=0;MQ0F=0;AC=1;AN=1;DP4=5,2,0,39;MQ=60 GT:PL 1:125,52
NC_045512.2 28271 . A T 228.427 . DP=308;VDB=0;SGB=-0.693147;RPBZ=2.82992;MQBZ=3.08661;MQSBZ=-5.14538;BQBZ=5.29899;SCBZ=-3.33492;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,3,259,45;MQ=59 GT:PL 1:255,0
NC_045512.2 28311 . C T 228.43 . DP=328;VDB=0;SGB=-0.693147;RPBZ=2.11906;MQBZ=-0.186245;MQSBZ=-5.32682;BQBZ=2.5282;SCBZ=-2.51243;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,265,62;MQ=59 GT:PL 1:255,0
NC_045512.2 28330 . A G 225.426 . DP=335;VDB=0;SGB=-0.693147;MQSBZ=-6.46363;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,265,68;MQ=59 GT:PL 1:255,0
NC_045512.2 28370 . A T 225.417 . DP=326;VDB=0;SGB=-0.693147;MQSBZ=-5.16398;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,240,9;MQ=59 GT:PL 1:255,0
NC_045512.2 28371 . G T 228.426 . DP=328;VDB=0;SGB=-0.693147;RPBZ=2.53987;MQBZ=4.87105;MQSBZ=-7.54472;BQBZ=1.93004;SCBZ=-3.2353;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,245,38;MQ=59 GT:PL 1:255,0
NC_045512.2 28881 . G A 225.426 . DP=183;VDB=0;SGB=-0.693147;MQSBZ=-0.378907;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,178;MQ=59 GT:PL 1:255,0
NC_045512.2 28882 . G A 225.426 . DP=183;VDB=0;SGB=-0.693147;MQSBZ=-0.378907;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,5,178;MQ=59 GT:PL 1:255,0
NC_045512.2 28883 . G C 228.428 . DP=183;VDB=0;SGB=-0.693147;RPBZ=-0.364254;MQBZ=-0.16758;MQSBZ=-0.378907;BQBZ=2.40729;SCBZ=0.155931;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,5,177;MQ=59 GT:PL 1:255,0
NC_045512.2 29136 . A C 50.1294 . DP=52;VDB=7.12062e-27;SGB=-0.693147;RPBZ=-7.13398;BQBZ=-0.361158;SCBZ=-2.76887;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,5,46,0;MQ=60 GT:PL 1:124,47
NC_045512.2 29510 . A C 228.429 . DP=257;VDB=0;SGB=-0.693147;RPBZ=-1.27353;MQBZ=-0.0885608;MQSBZ=-0.313595;BQBZ=1.97736;SCBZ=1.08328;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,12,244;MQ=59 GT:PL 1:255,0
NC_045512.2 29733 . CGAGGCCACGCGGAGTACGATCGAGTGTA CTA 225.422 . INDEL;IDV=246;IMF=0.991935;DP=248;VDB=0;SGB=-0.693147;RPBZ=-3.73042;SCBZ=0.203259;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,242;MQ=60 GT:PL 1:255,0