I am currently testing a development bioinformatics pipeline that uses BWA-MEM aligner.
For some reason, I was under the impression that the MAPQ (score for single end read) from BWA-MEM is capped at 60.
However, in a few samples I'm seeing a MAPQ of 70 in regions that show MAPQ = 60 in the rest of the samples.
Is this a potential bug in this development pipeline? Or does BWA-MEM really produce MAPQ values of 70? And is there literature available on this?