Dear Samtools-help people,
I would like to ask regarding a value reported in vcf output after SNP calling
process through mpileup. I've attached my sample output file if you want to see
in detail.
My question is that what is the meaning of a value called "QS", which states
"Auxiliary tag used for calling" from its description. I think it seems like
the variant frequency of base type in a certain position, but the value is not
equal when I've tried calculating by hand manually. Or is that a variant
frequency that is corrected by the error rate from raw fastq reads?
Thank you very much,
Teeratas
Teeratas Kijpornyongpan
MS Student
Department of Botany and Plant Pathology
Purdue University
West Lafayette, IN 47907
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.2+htslib-1.2.1
##samtoolsCommand=samtools mpileup -uD -g -f ./rDNA_reference/MCA5214rDNA.fa
5214rDNA-alignment.sorted.bam
##reference=file://./rDNA_reference/MCA5214rDNA.fa
##contig=<ID=5214_SSU_partial,length=1617>
##contig=<ID=5214_ITS,length=620>
##contig=<ID=5214_LSU_parital,length=1019>
##ALT=<ID=X,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 reads
supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of 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=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read
Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping
Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base
Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping
Quality vs Strand Bias (bigger is better)">
##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)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for
calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled
genotype likelihoods">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality
bases">
##bcftools_viewVersion=1.2+htslib-1.2.1
##bcftools_viewCommand=view -
##bcftools_viewCommand=view 5214rDNA-alignment-raw.bcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
5214rDNA-alignment.sorted.bam
5214_SSU_partial 1 . A <X> 0 .
DP=7999;I16=7999,0,0,0,296517,1.1069e+07,0,0,276108,1.0163e+07,0,0,174033,4.1408e+06,0,0;QS=1,0;MQ0F=0
PL:DP 0,255,255:7999
5214_SSU_partial 12 . A C,G,<X> 0 .
DP=8010;I16=8003,0,7,0,295723,1.10409e+07,110,1730,276370,1.01768e+07,222,7452,191455,4.65621e+06,175,4375;QS=0.999565,0.000312231,0.000122521,0;VDB=0.000524167;SGB=-0.636426;RPB=0.849607;MQB=0.698947;BQB=4.39969e-05;MQ0F=0
PL:DP 0,255,255,255,255,255,255,255,255,255:8010
5214_SSU_partial 24 . A G,C,<X> 0 .
DP=8021;I16=8016,0,4,0,298980,1.12233e+07,108,3400,276886,1.01981e+07,146,5572,196546,4.8481e+06,100,2500;QS=0.999632,0.000243,0.000125419,0;VDB=0.0320192;SGB=-0.556411;RPB=0.932333;MQB=0.903379;BQB=0.327101;MQ0F=0
PL:DP 0,255,255,255,255,255,255,255,255,255:8020
5214_SSU_partial 37 . C A,T,<X> 0 .
DP=8009;I16=7994,0,15,0,295345,1.10198e+07,457,15583,276561,1.01985e+07,553,21321,183620,4.43649e+06,375,9375;QS=0.998288,0.00146704,0.000244506,0;VDB=3.32167e-05;SGB=-0.688148;RPB=0.396565;MQB=0.700147;BQB=0.193482;MQ0F=0
PL:DP 0,255,255,255,255,255,255,255,255,255:8009
5214_SSU_partial 49 . G T,A,<X> 0 .
DP=7900;I16=7892,0,8,0,291443,1.08552e+07,250,8458,285404,1.08801e+07,250,8620,167879,4.00206e+06,120,2416;QS=0.999253,0.000600122,0.000147127,0;VDB=0.791433;SGB=-0.651104;RPB=0.932714;MQB=0.548051;BQB=0.071276;MQ0F=0
PL:DP 0,255,255,255,255,255,255,255,255,255:7900------------------------------------------------------------------------------
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