Bwa-Mem - Where Has Sm:I Gone?

Question

[steve]

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?

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EDIT:

These tags would also be nice:

XT; XA; X0;

Answer 1

[Istvan Albert]

The mapping quality is reported in the 5th column of the SAM file (MAPQ).

[steve]

So for BWA-MEM, is SM:i always equal to MAPQ? Is that why Heng removed this from the output? IF that's the case I can just duplicate the field. easy.

[Istvan Albert]

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

[amirmhzadeh]

Any thoughts on how MAPQ is assigned?