Off topic:MAPQ values are 60 in bwa mem

Question

[John]

Hi dear one,

I am getting lots of MAPQ values as 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 60 is the maximal limit!

IS there a trouble in calculating MAPQ thats why it is showing more 60?

Thanks in advance!