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bwa mem has more MAPQ values as 0 and 60

Hi dear one,

Why maximum no. of the MAPQ values are 0 and 60 in bwa mem?

I have ran the same read (paired end) in bowtie2 but it gave me good MAPQ values!

I know there is a difference in calculating MAPQ values between bowtie2 and bwa mem, but in bwa mem 0 and 60 are the minimal & maximal limit correspondingly!

Can you help me in this?

Thanks in advance!

bwamem bowtie2
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written by John John

1 answer

Here: Bwa Mapping Qualities Of 0

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written by Matteo Schiavinato Matteo Schiavinato

Yeah Thanks, Zero is fine! What about the MAPQ of 60?

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written by John John

okay, thanks, But,

Is it same to have 10000 no. of MAPQ as 42 in bowtie2 and 10000 no of MAPQ as 60 in BWA?

Here is my results:

In Bowtie2, 3167612 numbers of 0 MAPQ and 3575176 numbers of 42 MAPQ

In BWA MEM, 3178435 numbers of 0 MAPQ and 3644080 numbers of 60 MAPQ

Should I consider this 60 as best MAPQ in bwa mem? (since 42 is the best MAPQ in bowtie2)

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written by John John

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