Hie NGS Geeks,
Recently I observed some huge difference in mapping quality when aligned with bowtie & bwa, after alignment i called variants using samtools mpileup. I thought someone might enlighten my knowledge about this, so my observations are
1. With bowtie I got mapping quality 2 & quality 6.98 for particular position and when I called variants using samtools surprisingly it didn't report.
Particular position in VCF file for reference: "SL2.50ch01 559045 . G . 6.98 . DP=143;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,64,71;MQ=2;FQ=-282 PL:DP27:135"
2. but with bwa I got mapping quality 10 & quality 78 plus it reported variant i.e. alternate allele.
Particular position in VCF file for reference:"SL2.50ch01 559045 . G T 78 . DP=58;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,28,28;MQ=10;FQ=-196 GT:PL:DP:GQ 1/1:111,169,0:56:99".
I Think am not confusing anyone, if so please let me know & thanks in advance