I have a question about how VarFreq is calculated in pileup2snp.
I’ve got these results:
Chrom 1
Position 260300
Ref G
Cons R
Reads1 3
Reads2 6
VarFreq 50%
Strands1 1
Strands2 2
Qual1 42
Qual2 22
Pvalue 0.004525
MapQual1 1
MapQual2 1
Reads1Plus 3
Reads1Minus 0
Reads2Plus 4
Reads2Minus 2
VarAllele A
Shouldn’t VarFreq be #Reads2/(#Reads1 + #Reads2)=3/(3+6)=1/3?
and at another position I've got:
Reads1 0
Reads2 8
VarFreq 80%
What am I missing here?
Also, when I look at the bam file in tablet there are more than 100 reads. Why only 9 reads in output from pileup2snp?
Kind Regards
Petter
I’ve got these results:
Chrom 1
Position 260300
Ref G
Cons R
Reads1 3
Reads2 6
VarFreq 50%
Strands1 1
Strands2 2
Qual1 42
Qual2 22
Pvalue 0.004525
MapQual1 1
MapQual2 1
Reads1Plus 3
Reads1Minus 0
Reads2Plus 4
Reads2Minus 2
VarAllele A
Shouldn’t VarFreq be #Reads2/(#Reads1 + #Reads2)=3/(3+6)=1/3?
and at another position I've got:
Reads1 0
Reads2 8
VarFreq 80%
What am I missing here?
Also, when I look at the bam file in tablet there are more than 100 reads. Why only 9 reads in output from pileup2snp?
Kind Regards
Petter
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