Tophat/Bowtie does not yield mapping quality, so, as per the SAM spec, that field is set to 255, indicating that quality is unavailable. http://samtools.sourceforge.net/SAM1.pdf Best, J. On Feb 7, 2012, at 5:46 PM, Li, Jilong (MU-Student) wrote:

Hi all,

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.

Thanks!

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