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Copy pathUSA-MA-Broad_CRSP-01315-2021.bam_LoFreq.vcf
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USA-MA-Broad_CRSP-01315-2021.bam_LoFreq.vcf
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##fileformat=VCFv4.0
##fileDate=20210609
##source=/Users/lakras/2021_05_19_contamination_detection_from_minor_alleles/2021_06_01_polishing_software/software/lofreq_star-2.1.3.1/bin/lofreq call -f /Users/lakras/2021_05_19_contamination_detection_from_minor_alleles/2021_06_01_polishing_software/test_files/NC_045512.2.fasta -o /Users/lakras/2021_05_19_contamination_detection_from_minor_alleles/2021_06_01_polishing_software/intermediate/USA-MA-Broad_CRSP-01315-2021.align_to_ref.trimmed.bam_LoFreq.vcf /Users/lakras/2021_05_19_contamination_detection_from_minor_alleles/2021_06_01_polishing_software/test_files/cross_contamination_pair/USA-MA-Broad_CRSP-01315-2021.align_to_ref.trimmed.bam
##reference=/Users/lakras/2021_05_19_contamination_detection_from_minor_alleles/2021_06_01_polishing_software/test_files/NC_045512.2.fasta
##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_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_69,Description="Minimum SNV Quality (Phred) 69">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_045512.2 241 . C T 49314 PASS DP=2177;AF=0.997244;SB=3;DP4=1,0,1084,1087
NC_045512.2 1059 . C T 49314 PASS DP=5933;AF=0.995112;SB=5;DP4=17,0,5193,711
NC_045512.2 3037 . C T 49314 PASS DP=4926;AF=0.996346;SB=0;DP4=0,1,509,4399
NC_045512.2 3044 . C A 49314 PASS DP=5083;AF=0.995278;SB=8;DP4=0,20,551,4508
NC_045512.2 6762 . C T 49314 PASS DP=11834;AF=0.639344;SB=30;DP4=990,3254,1564,6002
NC_045512.2 7348 . T A 49314 PASS DP=2857;AF=0.998950;SB=0;DP4=1,0,1513,1341
NC_045512.2 8083 . G A 49314 PASS DP=4774;AF=0.990993;SB=3;DP4=32,0,4500,231
NC_045512.2 10319 . C T 49314 PASS DP=9601;AF=0.992084;SB=19;DP4=3,2,1064,8461
NC_045512.2 10681 . C T 240 PASS DP=4893;AF=0.013080;SB=11;DP4=880,3945,6,58
NC_045512.2 13119 . C T 49314 PASS DP=14086;AF=0.995314;SB=1;DP4=32,1,13146,874
NC_045512.2 14408 . C T 49314 PASS DP=4897;AF=0.993057;SB=36;DP4=15,6,1543,3320
NC_045512.2 14484 . C T 49314 PASS DP=5454;AF=0.997433;SB=7;DP4=1,1,554,4886
NC_045512.2 14805 . C T 49314 PASS DP=11082;AF=0.995849;SB=7;DP4=10,15,3114,7922
NC_045512.2 18131 . C T 49314 PASS DP=4283;AF=0.990427;SB=19;DP4=26,2,3004,1238
NC_045512.2 18424 . A G 49314 PASS DP=6277;AF=0.997929;SB=0;DP4=0,0,5551,713
NC_045512.2 19072 . G T 49314 PASS DP=6690;AF=0.996114;SB=3;DP4=6,2,3925,2739
NC_045512.2 19868 . C T 49314 PASS DP=3918;AF=0.999745;SB=4;DP4=1,0,1352,2565
NC_045512.2 21203 . A G 49314 PASS DP=3701;AF=0.997298;SB=0;DP4=0,0,2581,1110
NC_045512.2 21304 . C T 49314 PASS DP=2704;AF=0.996672;SB=14;DP4=2,0,511,2184
NC_045512.2 23403 . A G 49314 PASS DP=4670;AF=0.998715;SB=6;DP4=1,0,1041,3623
NC_045512.2 23656 . A T 146 PASS DP=9643;AF=0.008607;SB=149;DP4=3805,5747,69,14
NC_045512.2 25563 . G T 49314 PASS DP=14529;AF=0.998968;SB=4;DP4=3,7,2459,12055
NC_045512.2 25907 . G T 49314 PASS DP=1956;AF=0.986708;SB=4;DP4=9,15,553,1377
NC_045512.2 27964 . C T 49314 PASS DP=7055;AF=0.998299;SB=22;DP4=6,0,3010,4033
NC_045512.2 28472 . C T 49314 PASS DP=24716;AF=0.997532;SB=86;DP4=51,2,14845,9810
NC_045512.2 28869 . C T 47321 PASS DP=1401;AF=0.993576;SB=36;DP4=7,0,413,979
NC_045512.2 28928 . C T 874 PASS DP=1098;AF=0.065574;SB=17;DP4=216,809,24,48
NC_045512.2 28937 . C A 318 PASS DP=1062;AF=0.037665;SB=22;DP4=226,795,17,23
NC_045512.2 29360 . T C 49314 PASS DP=1757;AF=0.977234;SB=25;DP4=31,7,1632,85