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trim_ERR10002180_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_ERR10002180_sorted.bcf -f /home/focyte/DNA_Variant_Call/data/ref_genome/genome.fasta trim_ERR10002180_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_ERR10002180_sorted.vcf trim_ERR10002180_sorted.bcf; Date=Sat Sep 7 20:30:27 2024
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT trim_ERR10002180_sorted.bam
NC_045512.2 225 . C T 225.426 . DP=141;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,141,0;MQ=60 GT:PL 1:255,0
NC_045512.2 241 . C T 225.422 . DP=245;VDB=1;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,83,58;MQ=60 GT:PL 1:255,0
NC_045512.2 670 . T G 225.417 . DP=255;VDB=1;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,132,123;MQ=60 GT:PL 1:255,0
NC_045512.2 1150 . C T 169.421 . DP=54;VDB=7.00649e-45;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,54,0;MQ=60 GT:PL 1:199,0
NC_045512.2 1627 . C T 50.3969 . DP=251;VDB=0;SGB=-0.693147;RPBZ=-14.9009;BQBZ=1.13897;SCBZ=1.02416;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,107,137,7;MQ=60 GT:PL 1:255,177
NC_045512.2 2790 . C T 228.424 . DP=301;VDB=0;SGB=-0.693147;RPBZ=2.58084;BQBZ=-0.460257;SCBZ=0.422795;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,0,0,300;MQ=60 GT:PL 1:255,0
NC_045512.2 3037 . C T 225.422 . DP=258;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,258;MQ=60 GT:PL 1:255,0
NC_045512.2 3230 . G A 108.415 . DP=6;VDB=0.000595752;SGB=-0.616816;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,0;MQ=60 GT:PL 1:138,0
NC_045512.2 4184 . G A 54.4146 . DP=3;VDB=0.0221621;SGB=-0.511536;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,0;MQ=60 GT:PL 1:84,0
NC_045512.2 4321 . C T 228.416 . DP=259;VDB=0;SGB=-0.693147;RPBZ=7.29599;BQBZ=0.446652;SCBZ=-4.582;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,1,0,257;MQ=60 GT:PL 1:255,0
NC_045512.2 6979 . T G 197.367 . DP=149;VDB=0;SGB=-0.693147;RPBZ=2.63791;BQBZ=3.73659;SCBZ=-2.09979;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,8,0,138;MQ=60 GT:PL 1:224,0
NC_045512.2 9344 . C T 225.417 . DP=147;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,147,0;MQ=60 GT:PL 1:255,0
NC_045512.2 9424 . A G 225.426 . DP=220;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,220;MQ=60 GT:PL 1:255,0
NC_045512.2 9534 . C T 225.422 . DP=282;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,279;MQ=59 GT:PL 1:255,0
NC_045512.2 10029 . C T 225.426 . DP=277;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,277;MQ=59 GT:PL 1:255,0
NC_045512.2 10198 . C T 83.415 . DP=4;VDB=0.00911214;SGB=-0.556411;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,4,0;MQ=60 GT:PL 1:113,0
NC_045512.2 10447 . G A 225.417 . DP=270;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,264;MQ=60 GT:PL 1:255,0
NC_045512.2 10449 . C A 225.417 . DP=270;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,264;MQ=60 GT:PL 1:255,0
NC_045512.2 10889 . 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 11837 . G T 228.414 . DP=253;VDB=0;SGB=-0.693147;RPBZ=-0.15711;BQBZ=3.89947;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,6,1,245;MQ=60 GT:PL 1:255,0
NC_045512.2 12160 . G A 216.417 . DP=115;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,115;MQ=60 GT:PL 1:246,0
NC_045512.2 12880 . C T 225.417 . DP=256;VDB=0.891776;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,173,83;MQ=60 GT:PL 1:255,0
NC_045512.2 14408 . C T 225.422 . DP=296;VDB=0;SGB=-0.693147;MQSBZ=-0.117041;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,4,292;MQ=59 GT:PL 1:255,0
NC_045512.2 15714 . C T 225.422 . DP=184;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,184,0;MQ=60 GT:PL 1:255,0
NC_045512.2 16386 . C A 113.415 . DP=6;VDB=0.000411984;SGB=-0.616816;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,6,0;MQ=60 GT:PL 1:143,0
NC_045512.2 18163 . A G 225.417 . DP=149;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,149;MQ=60 GT:PL 1:255,0
NC_045512.2 19170 . C T 225.421 . DP=268;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,268;MQ=59 GT:PL 1:255,0
NC_045512.2 21520 . G T 103.138 . DP=35;VDB=2.12585e-11;SGB=-0.693079;RPBZ=3.0049;BQBZ=1.53333;SCBZ=-3.21216;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,6,0,29;MQ=60 GT:PL 1:137,7
NC_045512.2 21618 . C T 228.429 . DP=298;VDB=0;SGB=-0.693147;RPBZ=1.74598;MQBZ=-0.0580259;MQSBZ=-0.770443;BQBZ=1.83971;SCBZ=-1.7978;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,111,186;MQ=59 GT:PL 1:255,0
NC_045512.2 21764 . ATACATGT AT 228.424 . INDEL;IDV=141;IMF=0.986014;DP=143;VDB=0;SGB=-0.693147;RPBZ=0;SCBZ=0.169022;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,0,141;MQ=60 GT:PL 1:255,0
NC_045512.2 21987 . G A 214.417 . DP=102;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,102,0;MQ=60 GT:PL 1:244,0
NC_045512.2 22200 . T G 228.406 . DP=317;VDB=0;SGB=-0.693147;RPBZ=1.13714;BQBZ=4.81499;SCBZ=-2.53407;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,6,77,234;MQ=60 GT:PL 1:255,0
NC_045512.2 22578 . G A 174.416 . DP=60;VDB=1.26117e-44;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,60,0;MQ=60 GT:PL 1:204,0
NC_045512.2 22674 . C T 228.428 . DP=199;VDB=0;SGB=-0.693147;RPBZ=-0.0843879;BQBZ=2.20131;SCBZ=0.176292;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,198;MQ=60 GT:PL 1:255,0
NC_045512.2 22679 . T C 225.422 . DP=199;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,199;MQ=60 GT:PL 1:255,0
NC_045512.2 22686 . C T 225.422 . DP=199;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,199;MQ=60 GT:PL 1:255,0
NC_045512.2 22688 . A G 225.422 . DP=199;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,199;MQ=60 GT:PL 1:255,0
NC_045512.2 22775 . G A 225.417 . DP=224;VDB=9.1734e-30;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,22,202;MQ=60 GT:PL 1:255,0
NC_045512.2 22786 . A C 227.953 . DP=224;VDB=1.92216e-13;SGB=-0.693147;RPBZ=-2.21031;BQBZ=-0.823864;SCBZ=0.431836;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,46,22,156;MQ=60 GT:PL 1:255,0
NC_045512.2 22813 . G T 167.416 . DP=22;VDB=1.30483e-15;SGB=-0.692562;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,22,0;MQ=60 GT:PL 1:197,0
NC_045512.2 22879 . C T 163.416 . DP=22;VDB=1.30483e-15;SGB=-0.692562;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,22,0;MQ=60 GT:PL 1:193,0
NC_045512.2 22882 . T G 166.416 . DP=22;VDB=1.30483e-15;SGB=-0.692562;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,22,0;MQ=60 GT:PL 1:196,0
NC_045512.2 22917 . T G 166.416 . DP=22;VDB=1.30483e-15;SGB=-0.692562;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,22,0;MQ=60 GT:PL 1:196,0
NC_045512.2 22992 . G A 225.417 . DP=231;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,230,1;MQ=60 GT:PL 1:255,0
NC_045512.2 22995 . C A 225.417 . DP=231;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,230,1;MQ=60 GT:PL 1:255,0
NC_045512.2 23013 . A C 225.417 . DP=231;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,230,1;MQ=60 GT:PL 1:255,0
NC_045512.2 23018 . T G 228.424 . DP=231;VDB=0;SGB=-0.693147;RPBZ=8.79405;BQBZ=5.73195;SCBZ=-8.79405;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,230,0;MQ=60 GT:PL 1:255,0
NC_045512.2 23055 . A G 225.422 . DP=231;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,230,1;MQ=60 GT:PL 1:255,0
NC_045512.2 23063 . A T 225.417 . DP=231;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,230,1;MQ=60 GT:PL 1:255,0
NC_045512.2 23075 . T C 225.417 . DP=231;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,230,1;MQ=60 GT:PL 1:255,0
NC_045512.2 23403 . A G 225.422 . DP=143;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,143,0;MQ=60 GT:PL 1:255,0
NC_045512.2 23525 . C T 225.422 . DP=140;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,140;MQ=60 GT:PL 1:255,0
NC_045512.2 23599 . T G 228.424 . DP=251;VDB=1;SGB=-0.693147;RPBZ=-1.00284;BQBZ=2.74037;SCBZ=0.381092;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,105,145;MQ=60 GT:PL 1:255,0
NC_045512.2 23604 . C A 228.424 . DP=251;VDB=1;SGB=-0.693147;RPBZ=0.242542;BQBZ=2.97963;SCBZ=-2.89395;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,105,145;MQ=60 GT:PL 1:255,0
NC_045512.2 23854 . C A 67.6713 . DP=244;VDB=0;SGB=-0.693147;RPBZ=13.7957;BQBZ=-1.76432;SCBZ=2.4591;FS=0;MQ0F=0;AC=1;AN=1;DP4=76,0,0,168;MQ=60 GT:PL 1:180,85
NC_045512.2 23948 . G T 193.416 . DP=79;VDB=2.8026e-45;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,79,0;MQ=60 GT:PL 1:223,0
NC_045512.2 24424 . A T 188.37 . DP=150;VDB=0;SGB=-0.693147;RPBZ=4.09142;BQBZ=3.19384;SCBZ=-4.41977;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,8,0,142;MQ=60 GT:PL 1:215,0
NC_045512.2 24469 . T A 228.426 . DP=270;VDB=7.08626e-29;SGB=-0.693147;RPBZ=1.31189;MQBZ=11.5758;MQSBZ=-0.707107;BQBZ=2.27999;SCBZ=-0.602046;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,90,178;MQ=59 GT:PL 1:255,0
NC_045512.2 25000 . C T 228.433 . DP=198;VDB=0;SGB=-0.693147;RPBZ=3.95294;BQBZ=1.74639;SCBZ=-5.24983;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,197;MQ=60 GT:PL 1:255,0
NC_045512.2 25584 . C T 228.434 . DP=264;VDB=0;SGB=-0.693147;RPBZ=3.59995;BQBZ=2.40561;SCBZ=-4.9839;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,263;MQ=60 GT:PL 1:255,0
NC_045512.2 26060 . C T 225.417 . DP=191;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,191,0;MQ=60 GT:PL 1:255,0
NC_045512.2 26270 . C T 225.422 . DP=258;VDB=2.33337e-06;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,127,131;MQ=60 GT:PL 1:255,0
NC_045512.2 26529 . G A 225.417 . DP=158;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,158;MQ=60 GT:PL 1:255,0
NC_045512.2 26577 . C G 225.417 . DP=166;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,166;MQ=60 GT:PL 1:255,0
NC_045512.2 26709 . G A 198.416 . DP=88;VDB=9.80909e-45;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,88,0;MQ=60 GT:PL 1:228,0
NC_045512.2 27038 . A G 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 27807 . C T 225.417 . DP=252;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,195,57;MQ=60 GT:PL 1:255,0
NC_045512.2 27889 . C T 225.417 . DP=195;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,195,0;MQ=60 GT:PL 1:255,0
NC_045512.2 28271 . A T 228.41 . DP=151;VDB=0;SGB=-0.693147;RPBZ=1.21661;BQBZ=1.24813;SCBZ=-1.41691;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,1,117,32;MQ=60 GT:PL 1:255,0
NC_045512.2 28311 . C T 225.422 . DP=155;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,118,37;MQ=60 GT:PL 1:255,0
NC_045512.2 28330 . A G 225.426 . DP=155;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,118,37;MQ=60 GT:PL 1:255,0
NC_045512.2 28361 . GGAGAACGCAG GG 228.407 . INDEL;IDV=152;IMF=0.980645;DP=155;VDB=0;SGB=-0.693147;RPBZ=1.83708;SCBZ=-2.05435;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,2,117,30;MQ=60 GT:PL 1:255,0
NC_045512.2 28881 . G A 225.426 . DP=285;VDB=0;SGB=-0.693147;MQSBZ=-0.146122;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,282;MQ=59 GT:PL 1:255,0
NC_045512.2 28882 . G A 225.422 . DP=285;VDB=0;SGB=-0.693147;MQSBZ=-0.146122;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,282;MQ=59 GT:PL 1:255,0
NC_045512.2 28883 . G C 225.417 . DP=285;VDB=0;SGB=-0.693147;MQSBZ=-0.146122;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,282;MQ=59 GT:PL 1:255,0
NC_045512.2 29510 . A C 228.425 . DP=258;VDB=0;SGB=-0.693147;RPBZ=-0.134251;BQBZ=3.54068;SCBZ=0.178858;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,3,254;MQ=60 GT:PL 1:255,0