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‎bcftools_filtered_vcfs/SRR10903401.bam.vcf.filtered

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##bcftoolsVersion=1.9+htslib-1.9
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##bcftoolsCommand=mpileup -B -C 50 -d 250 --fasta-ref covid19-refseq.fasta --threads 10 -Ou SRR10903401.fq.sam.sorted.bam.rmdup
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##reference=file://covid19-refseq.fasta
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##contig=<ID=NC_045512.2,length=29903>
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##ALT=<ID=*,Description="Represents allele(s) other than observed.">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
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##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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##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">
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##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
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##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
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##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
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##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
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##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
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##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
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##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
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##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
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##bcftools_callVersion=1.9+htslib-1.9
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##bcftools_callCommand=call -mv -Ov -o SRR10903401.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:34:44 2020
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##bcftools_filterVersion=1.9+htslib-1.9
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##bcftools_filterCommand=filter '-e%QUAL<10 ||(RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3' SRR10903401.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:52:08 2020
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR10903401.fq.sam.sorted.bam.rmdup
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NC_045512.2 13325 . ACAACTTGTGC ACAACTTGTGCAACTTGTGC 12.6563 PASS INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=42 GT:PL 1/1:42,3,0

‎bcftools_filtered_vcfs/SRR10903402.bam.vcf.filtered

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##bcftoolsVersion=1.9+htslib-1.9
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##bcftoolsCommand=mpileup -B -C 50 -d 250 --fasta-ref covid19-refseq.fasta --threads 10 -Ou SRR10903402.fq.sam.sorted.bam.rmdup
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##reference=file://covid19-refseq.fasta
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##contig=<ID=NC_045512.2,length=29903>
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##ALT=<ID=*,Description="Represents allele(s) other than observed.">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
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##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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##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">
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##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
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##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
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##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
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##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
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##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
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##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
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##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
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##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
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##bcftools_callVersion=1.9+htslib-1.9
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##bcftools_callCommand=call -mv -Ov -o SRR10903402.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:34:45 2020
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##bcftools_filterVersion=1.9+htslib-1.9
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##bcftools_filterCommand=filter '-e%QUAL<10 ||(RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3' SRR10903402.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:52:08 2020
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR10903402.fq.sam.sorted.bam.rmdup
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NC_045512.2 1526 . GCCTATTGGGTTCC GCC 10.7919 PASS INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=40 GT:PL 1/1:40,3,0
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NC_045512.2 12643 . TA TACGCA 10.7919 PASS INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=40 GT:PL 1/1:40,3,0
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NC_045512.2 26062 . GGTGTTG GGTGTTGTGTTG 12.6563 PASS INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=2;AN=2;DP4=0,0,0,1;MQ=42 GT:PL 1/1:42,3,0

‎bcftools_filtered_vcfs/SRR10971381.bam.vcf.filtered

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##bcftoolsVersion=1.9+htslib-1.9
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##bcftoolsCommand=mpileup -B -C 50 -d 250 --fasta-ref covid19-refseq.fasta --threads 10 -Ou SRR10971381.fq.sam.sorted.bam.rmdup
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##reference=file://covid19-refseq.fasta
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##contig=<ID=NC_045512.2,length=29903>
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##ALT=<ID=*,Description="Represents allele(s) other than observed.">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
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##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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##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">
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##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
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##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
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##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
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##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
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##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
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##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
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##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
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##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
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##bcftools_callVersion=1.9+htslib-1.9
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##bcftools_callCommand=call -mv -Ov -o SRR10971381.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:35:23 2020
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##bcftools_filterVersion=1.9+htslib-1.9
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##bcftools_filterCommand=filter '-e%QUAL<10 ||(RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3' SRR10971381.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:52:08 2020
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR10971381.fq.sam.sorted.bam.rmdup

‎bcftools_filtered_vcfs/SRR11059940.bam.vcf.filtered

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##bcftoolsVersion=1.9+htslib-1.9
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##bcftoolsCommand=mpileup -B -C 50 -d 250 --fasta-ref covid19-refseq.fasta --threads 10 -Ou SRR11059940.fq.sam.sorted.bam.rmdup
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##reference=file://covid19-refseq.fasta
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##contig=<ID=NC_045512.2,length=29903>
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##ALT=<ID=*,Description="Represents allele(s) other than observed.">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
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##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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##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">
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##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
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##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
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##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
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##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
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##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
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##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
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##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
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##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
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##bcftools_callVersion=1.9+htslib-1.9
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##bcftools_callCommand=call -mv -Ov -o SRR11059940.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:35:23 2020
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##bcftools_filterVersion=1.9+htslib-1.9
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##bcftools_filterCommand=filter '-e%QUAL<10 ||(RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3' SRR11059940.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:52:08 2020
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR11059940.fq.sam.sorted.bam.rmdup
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NC_045512.2 7866 . G T 220 PASS DP=244;VDB=0.615418;SGB=-0.693147;RPB=0.0659214;MQB=0.988841;MQSB=0.546054;BQB=0.997154;MQ0F=0.0163934;ICB=1;HOB=0.5;AC=1;AN=2;DP4=24,20,117,83;MQ=39 GT:PL 0/1:255,0,71

‎bcftools_filtered_vcfs/SRR11059941.bam.vcf.filtered

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##bcftoolsVersion=1.9+htslib-1.9
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##bcftoolsCommand=mpileup -B -C 50 -d 250 --fasta-ref covid19-refseq.fasta --threads 10 -Ou SRR11059941.fq.sam.sorted.bam.rmdup
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##reference=file://covid19-refseq.fasta
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##contig=<ID=NC_045512.2,length=29903>
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##ALT=<ID=*,Description="Represents allele(s) other than observed.">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
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##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
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##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">
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##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
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##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
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##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
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##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
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##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
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##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
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##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
24+
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
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##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
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##bcftools_callVersion=1.9+htslib-1.9
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##bcftools_callCommand=call -mv -Ov -o SRR11059941.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:35:31 2020
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##bcftools_filterVersion=1.9+htslib-1.9
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##bcftools_filterCommand=filter '-e%QUAL<10 ||(RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3' SRR11059941.fq.sam.sorted.bam.rmdup.vcf; Date=Thu Mar 26 16:52:08 2020
31+
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR11059941.fq.sam.sorted.bam.rmdup

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