This question is a follow up from: Are some sequences uniquely mapped by BWA when mapped as paired-end that would not be when mapped as single-end?
My question is:
How does BWA-MEM report single-end mapping quality?
BWA-backtrack kindly reports the single-end mapping quality using the SM:i tag. But is there a way (hackish or otherwise) to get BWA-MEM to report this field? If not, why?
EDIT:
These tags would also be nice:
XT; XA; X0;
•
written
by
steve •
1 answer
The mapping quality is reported in the 5th column of the SAM file (MAPQ).
these are slightly different meanings of mapping qualities some discussion is here
Differing BWA MAPQ scores for a read depending on how I build the transcriptome
the way mapping qualities are obtained are somewhat mysterious and perhaps it is better there is only one of them
Any thoughts on how MAPQ is assigned?
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