bwa mem has more MAPQ values as 0 and 60

Question

[John]

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!

[WouterDeCoster]

See also MAPQ values are really useful but their implementation is a mess

Answer 1

[Matteo Schiavinato]

Here: Bwa Mapping Qualities Of 0

[John]

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

[Matteo Schiavinato]

Same concept, on the other end of the scale!

[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)

[Matteo Schiavinato]

Yes, you should consider it as the best.