trim_ERR10001396_sorted.vcf

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##bcftoolsVersion=1.13+htslib-1.13+ds
##bcftoolsCommand=mpileup -O b -o trim_ERR10001396_sorted.bcf -f /home/focyte/DNA_Variant_Call/data/ref_genome/genome.fasta trim_ERR10001396_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_ERR10001396_sorted.vcf trim_ERR10001396_sorted.bcf; Date=Sat Sep  7 20:32:28 2024
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	trim_ERR10001396_sorted.bam
NC_045512.2	25	.	T	A	135.967	.	DP=33;VDB=1.5958e-15;SGB=-0.692976;RPBZ=-4.19264;MQBZ=-0.518875;MQSBZ=-1.51658;BQBZ=1.89866;FS=0;MQ0F=0;AC=1;AN=1;DP4=6,1,17,9;MQ=59	GT:PL	1:255,92
NC_045512.2	670	.	T	G	225.417	.	DP=255;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,253,2;MQ=60	GT:PL	1:255,0
NC_045512.2	1593	.	C	T	225.426	.	DP=258;VDB=0.000157033;SGB=-0.693147;MQSBZ=-1.01069;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,87,171;MQ=59	GT:PL	1:255,0
NC_045512.2	2483	.	A	T	38.7938	.	DP=8;VDB=0.00187095;SGB=-0.590765;RPBZ=-2.58199;BQBZ=1.23468;SCBZ=-2.58199;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,5,0;MQ=60	GT:PL	1:98,32
NC_045512.2	3037	.	C	T	172.416	.	DP=52;VDB=2.1842e-41;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,52;MQ=60	GT:PL	1:202,0
NC_045512.2	3385	.	TAAAAA	TAAA	60.0828	.	INDEL;IDV=16;IMF=0.313726;DP=51;VDB=1.12104e-44;SGB=-0.689466;RPBZ=3.51571;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,35,0,16;MQ=60	GT:PL	1:141,53
NC_045512.2	3412	.	TAAAAA	TAA	7.31824	.	INDEL;IDV=9;IMF=0.176471;DP=51;VDB=1.23314e-43;SGB=-0.662043;RPBZ=5.95627;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,42,0,9;MQ=60	GT:PL	1:52,17
NC_045512.2	3683	.	C	A	138.42	.	DP=12;VDB=2.26006e-08;SGB=-0.680642;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,12,0;MQ=60	GT:PL	1:201,33
NC_045512.2	4184	.	G	A	225.417	.	DP=136;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,136,0;MQ=60	GT:PL	1:255,0
NC_045512.2	9344	.	C	T	143.416	.	DP=10;VDB=0.702735;SGB=-0.670168;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,10,0;MQ=60	GT:PL	1:173,0
NC_045512.2	9424	.	A	G	225.426	.	DP=276;VDB=0;SGB=-0.693147;MQSBZ=-0.105021;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,272;MQ=59	GT:PL	1:255,0
NC_045512.2	9534	.	C	T	225.417	.	DP=297;VDB=0;SGB=-0.693147;MQSBZ=3.31317;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,8,289;MQ=59	GT:PL	1:255,0
NC_045512.2	10029	.	C	T	225.422	.	DP=261;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,261;MQ=60	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=263;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,256;MQ=60	GT:PL	1:255,0
NC_045512.2	10449	.	C	A	225.417	.	DP=263;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,256;MQ=60	GT:PL	1:255,0
NC_045512.2	11000	.	A	C	90.4185	.	DP=7;VDB=6.71664e-05;SGB=-0.636426;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,7,0;MQ=60	GT:PL	1:168,48
NC_045512.2	11235	.	C	T	153.425	.	DP=31;VDB=2.51782e-13;SGB=-0.69311;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,31;MQ=60	GT:PL	1:183,0
NC_045512.2	11287	.	GTCTGGTTTT	G	187.387	.	INDEL;IDV=39;IMF=0.847826;DP=46;VDB=9.02549e-16;SGB=-0.693144;RPBZ=-0.352505;MQBZ=2.36039;SCBZ=0.156668;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,3,0,39;MQ=60	GT:PL	1:214,0
NC_045512.2	12880	.	C	T	225.417	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	14408	.	C	T	225.417	.	DP=243;VDB=2.26394e-06;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,83,160;MQ=60	GT:PL	1:255,0
NC_045512.2	15714	.	C	T	172.416	.	DP=43;VDB=6.3643e-25;SGB=-0.693146;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,43,0;MQ=60	GT:PL	1:202,0
NC_045512.2	16935	.	G	A	228.423	.	DP=251;VDB=0;SGB=-0.693147;RPBZ=-0.0179698;BQBZ=-0.339502;SCBZ=0.109983;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,250;MQ=60	GT:PL	1:255,0
NC_045512.2	17410	.	C	T	83.415	.	DP=4;VDB=0.00701511;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	21294	.	T	G	74.9676	.	DP=10;VDB=1.33331e-05;SGB=-0.651104;SCBZ=-2;FS=0;MQ0F=0;AC=1;AN=1;DP4=2,0,8,0;MQ=60	GT:PL	1:141,39
NC_045512.2	21618	.	C	T	225.422	.	DP=300;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,180,120;MQ=60	GT:PL	1:255,0
NC_045512.2	21764	.	ATACATGT	AT	207.4	.	INDEL;IDV=82;IMF=0.97619;DP=84;VDB=8.40779e-45;SGB=-0.693147;RPBZ=0.208852;SCBZ=0.22219;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,2,0,82;MQ=60	GT:PL	1:234,0
NC_045512.2	21987	.	G	A	225.417	.	DP=167;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,167,0;MQ=60	GT:PL	1:255,0
NC_045512.2	22200	.	T	G	228.422	.	DP=283;VDB=0;SGB=-0.693147;RPBZ=0.267189;BQBZ=4.43325;SCBZ=-1.32447;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,1,145,136;MQ=60	GT:PL	1:255,0
NC_045512.2	22578	.	G	A	217.421	.	DP=140;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,140,0;MQ=60	GT:PL	1:247,0
NC_045512.2	22674	.	C	T	212.417	.	DP=110;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,110;MQ=60	GT:PL	1:242,0
NC_045512.2	22679	.	T	C	214.417	.	DP=110;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,110;MQ=60	GT:PL	1:244,0
NC_045512.2	22686	.	C	T	215.417	.	DP=105;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,105;MQ=60	GT:PL	1:245,0
NC_045512.2	22688	.	A	G	208.421	.	DP=111;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,111;MQ=60	GT:PL	1:238,0
NC_045512.2	22775	.	G	A	223.417	.	DP=112;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,112;MQ=60	GT:PL	1:253,0
NC_045512.2	22786	.	A	C	5.85156	.	DP=110;VDB=0;SGB=-0.693147;BQBZ=-1.07394;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,40,0,70;MQ=60	GT:PL	1:169,137
NC_045512.2	22992	.	G	A	225.417	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	22995	.	C	A	225.417	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	23013	.	A	C	228.426	.	DP=250;VDB=0;SGB=-0.693147;RPBZ=0.0520559;BQBZ=4.47172;SCBZ=0.127255;FS=0;MQ0F=0;AC=1;AN=1;DP4=2,0,248,0;MQ=60	GT:PL	1:255,0
NC_045512.2	23018	.	T	G	225.417	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	23055	.	A	G	225.422	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	23063	.	A	T	225.422	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	23075	.	T	C	225.422	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,250,0;MQ=60	GT:PL	1:255,0
NC_045512.2	23114	.	C	T	225.422	.	DP=250;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,248,1;MQ=60	GT:PL	1:255,0
NC_045512.2	23403	.	A	G	62.4147	.	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	1:92,0
NC_045512.2	23525	.	C	T	62.4147	.	DP=3;VDB=0.0221621;SGB=-0.511536;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,0,3;MQ=60	GT:PL	1:92,0
NC_045512.2	23599	.	T	G	225.417	.	DP=252;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,249,3;MQ=60	GT:PL	1:255,0
NC_045512.2	23604	.	C	A	225.417	.	DP=252;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,249,3;MQ=60	GT:PL	1:255,0
NC_045512.2	23948	.	G	T	225.417	.	DP=173;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,173,0;MQ=60	GT:PL	1:255,0
NC_045512.2	24424	.	A	T	197.409	.	DP=132;VDB=0;SGB=-0.693147;RPBZ=2.85381;BQBZ=2.8498;SCBZ=-3.26784;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,4,0,128;MQ=60	GT:PL	1:224,0
NC_045512.2	24469	.	T	A	225.422	.	DP=254;VDB=3.27778e-22;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,114,140;MQ=60	GT:PL	1:255,0
NC_045512.2	25000	.	C	T	225.422	.	DP=168;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,1,167;MQ=60	GT:PL	1:255,0
NC_045512.2	25584	.	C	T	225.422	.	DP=254;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,1,253;MQ=60	GT:PL	1:255,0
NC_045512.2	26060	.	C	T	133.416	.	DP=9;VDB=0.000442467;SGB=-0.662043;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,9,0;MQ=60	GT:PL	1:163,0
NC_045512.2	26270	.	C	T	228.428	.	DP=282;VDB=0;SGB=-0.693147;RPBZ=-0.756172;MQBZ=-0.059655;MQSBZ=-0.134352;BQBZ=-0.495214;SCBZ=0.337913;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,5,276;MQ=59	GT:PL	1:255,0
NC_045512.2	26529	.	G	A	225.417	.	DP=263;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,2,261;MQ=60	GT:PL	1:255,0
NC_045512.2	26577	.	C	G	225.417	.	DP=265;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,2,263;MQ=60	GT:PL	1:255,0
NC_045512.2	26709	.	G	A	119.415	.	DP=7;VDB=0.0402698;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	27807	.	C	T	225.417	.	DP=252;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,249;MQ=60	GT:PL	1:255,0
NC_045512.2	27889	.	C	T	155.416	.	DP=6;VDB=0.999147;SGB=-0.616816;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,3,3;MQ=60	GT:PL	1:185,0
NC_045512.2	27904	.	T	G	150.31	.	DP=250;VDB=0;SGB=-0.693147;RPBZ=-14.3411;BQBZ=-2.74492;FS=0;MQ0F=0;AC=1;AN=1;DP4=3,9,0,238;MQ=60	GT:PL	1:177,0
NC_045512.2	28271	.	A	T	228.425	.	DP=265;VDB=0;SGB=-0.693147;RPBZ=-0.230848;BQBZ=3.85183;SCBZ=0.217709;FS=0;MQ0F=0;AC=1;AN=1;DP4=1,0,262,2;MQ=60	GT:PL	1:255,0
NC_045512.2	28311	.	C	T	225.417	.	DP=268;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,266,2;MQ=60	GT:PL	1:255,0
NC_045512.2	28681	.	G	T	225.417	.	DP=243;VDB=0;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,243,0;MQ=60	GT:PL	1:255,0
NC_045512.2	28881	.	G	A	225.417	.	DP=250;VDB=2.65963e-29;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,218,32;MQ=60	GT:PL	1:255,0
NC_045512.2	28882	.	G	A	225.417	.	DP=250;VDB=7.26718e-29;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,218,32;MQ=60	GT:PL	1:255,0
NC_045512.2	28883	.	G	C	225.422	.	DP=250;VDB=3.67067e-29;SGB=-0.693147;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,218,32;MQ=60	GT:PL	1:255,0
NC_045512.2	29510	.	A	C	225.417	.	DP=248;VDB=0.99994;SGB=-0.693147;MQSBZ=-0.767948;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,0,92,156;MQ=59	GT:PL	1:255,0
NC_045512.2	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	228.426	.	INDEL;IDV=178;IMF=0.978022;DP=182;VDB=0;SGB=-0.693147;RPBZ=-2.969;MQBZ=-0.149906;SCBZ=0.511208;FS=0;MQ0F=0;AC=1;AN=1;DP4=0,1,0,176;MQ=60	GT:PL	1:255,0