SHRiMP mapping qualities

[BambooGarden]

Hello everyone,

I aligned SOLiD reads to a reference genome using SHRiMP2 and I am
looking at the alignment in IGV.

What I find weird is that either the reads have a mapping score of 250 (even
if there are mutations in them) or a mapping score of 0. There are entire
regions of 1-2 kb where all reads have a mapping quality of 0. Those regions
also have a very high coverage (up to 700x, whereas the average is about 30x).

Any idea why this is happening?

Thanks in advance