This actually does not seem to hold upon checking (or at least not anymore). In Tophat 1.4.1, there is no mapping quality of 2. I've looked at a large number of BAM files and it seems that the qualities are as follows:
- 255 = unique mapping
- 3 = maps to 2 locations in the target
- 1 = maps to 3-4 locations
- 0 = maps to 5 or more locations (up to the number defined in "--prefilter-multihits").
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.
I think this is correct, it fits with what I have observed.
My tophat output bam file is using 50 to indicate the unique mapping, is there any official matrials about the mapping quality of unique mapped reads?
In tophat website http://tophat.cbcb.umd.edu/, it says that "most of the optional SAM fields (AS, MD, NM, and etc.) generated by Bowtie 2 are now reported by TopHat as well (reconstructed as necessary)".
And in bowtie2 website http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#mapping-quality-higher-more-unique, it says that "Mapping quality: higher = more unique".
However, I cannot find the exact mapping quality number for unique mapped reads