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