This is not strictly correct. 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.
Date: Tue, 7 Feb 2012 17:56:34 -0500
From: Jeremy Goecks email@example.com
To: "Li, Jilong (MU-Student)" firstname.lastname@example.org
Cc: "email@example.com" firstname.lastname@example.org
Subject: Re: [galaxy-user] about Mapping Quality
Content-Type: text/plain; charset="us-ascii"
Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that field is set to 255, indicating that quality is unavailable.
On Feb 7, 2012, at 5:46 PM, Li, Jilong (MU-Student) wrote:
I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file,
the value of some mapping quality (the 5th column) is 255. What does it mean? And I found these reads which have mapping quality 255 mapped to unique place.
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