Why some reads have MAPQ = 0 with bwa and look good?

Question

[lacb]

Hi,

I aligned exomes data to the human hg38 genome with bwa.

Now it happen I have reads with MAPQ 0 when I look at the alignments in IGV (pale colored reads).

For example in the following screenshot, a few reads in the chrM have a MAPQ of 0 but the bases looks correct (1-2 mismatch or variants).

What does this means? The reads are marked as "Primary", how do I know if they map better somewhere else?

Answer 1

[acvill]

What Does The Zero Mapping Quality Mean For The Bwa Mapper?