I have simulated short reads (<100bp) and trying to align to my reference using BWA_aln and I had a question when I saw my results. Most of my reads are mapping correctly and perfectly to the reference (90 matches out of 90 bp for example) but the MapQ is still equal to 0. Do you have any idea why is that happening ?
As those reads are simulated I know that they are correctly map aswell though.
Thanks a lot,