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bowtie2 MAPQ scores more than 42

I'm using bowtie2 (-very-fast-local) to align RNA-Seq reads, and according to all the information I can find online the maximum MAPQ score should be 42:

Nevertheless, I'm getting a lot of alignments with a MAPQ score of 44, more than 42. Any idea how/why?

Histogram of MAPQ scores after filtering for at least 40

mapq bowtie2
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written by rakusmaximus • rakusmaximus

1 answer

https://github.com/BenLangmead/bowtie2/issues/357

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written by ATpoint ATpoint

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