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SHRiMP mapping qualities



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  • 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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