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Old 12-09-2013, 02:36 AM   #1
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Location: Denmark

Join Date: Nov 2013
Posts: 5
Default SHRiMP mapping qualities

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
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