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  • bowtie SAM mapq field

    I am trying to find out how bowtie mapq field is computed:

    From the bowtie manual:

    If an alignment is non-repetitive (according to -m, --strata and other options) set the MAPQ (mapping quality) field to this value. See the SAM Spec for details about the MAPQ field Default: 255.

    If i map data with, for example, -m 10, i am allowing up to 10 multiple hits per read. How is the reported SAM mapq number connected with the number of multiple hits of an alignment? If a read has a single hit (from the manual), mapq = 255. If a read has 5 multiple hits, mapq=?

    SAM documentation doesn't tell me anything more (only that it is phread-scaled):

    MAPping Quality (phred-scaled posterior probability that the mapping position of this read is incorrect)

    In the end i would like to do something like this:

    samtools view -q 100 result.sam (filter out results with mapq <100)

    tnx for any help,
    Gregor

  • #2
    Tophat/bowtie don’t report mapping quality values that are as meaningful as BWA, but there is some information in the mapping quality values tophat reports. Tophat yields 4 distinct values for its mapping quality values (you can do a “unique” count on the mapping quality field of any SAM file from tophat to verify this):



    255 = unique mapping

    3 = maps to 2 locations in the target

    2 = maps to 3 locations

    1 = maps to 4-9 locations

    0 = maps to 10 or more locations.



    Except for the 255 case, the simple rule that was encoded by the authors is the usual phred quality scale:



    MapQ = -10 log10(P)



    Where P = probability that this mapping is NOT the correct one. The authors ignore the number of mismatches in this calculation and simply assume that if it maps to 2 locations then P = 0.5, 3 locations implies P = 2/3, 4 locations => P = 3/4 etc.



    As you can clearly see, then MapQ = -10 log10(0.5) = 3; -10 log10(2/3) = 1.76 (rounds to 2);

    -10 log10(3/4) = 1.25 (rounds to 1), etc.

    Comment


    • #3
      I think it is safe to say that bowtie does the same.

      Comment

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