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?
These tags would also be nice:
XT; XA; X0;