Hello,
I used bwa mem to align 125bp single end reads to human decoy reference genome. I know bwa will assign mapping quality as zero when one read mapped to two or more locations in the genome. However, I noticed some reads which are mapped equally well to different genomic locations, e.g. one read is mapped to equally well to autosome chromosome (chr16) and one of the patches (GL000192). CIGAR for both alignments are 125M. However, mapping quality for the alignment on chr16 is 23, while the alignment mapped to GL000192 got mapping quality of zero. I thought both of them should have mapping quality as zero? Is this right or not?
thanks!
I used bwa mem to align 125bp single end reads to human decoy reference genome. I know bwa will assign mapping quality as zero when one read mapped to two or more locations in the genome. However, I noticed some reads which are mapped equally well to different genomic locations, e.g. one read is mapped to equally well to autosome chromosome (chr16) and one of the patches (GL000192). CIGAR for both alignments are 125M. However, mapping quality for the alignment on chr16 is 23, while the alignment mapped to GL000192 got mapping quality of zero. I thought both of them should have mapping quality as zero? Is this right or not?
thanks!
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