Mapping quality: bad and normal

[serge2016]

Hello!

Dear authors, could you provide some kind of borders for the mapping quality bwa-mem2 produces?

Here (http://www.acgt.me/blog/2015/3/17/more-madness-with-mapq-scores-aka-why-bioinformaticians-hate-poor-and-incomplete-software-documentation#:~:text=BWA%20generates%20MAPQ%20scores%20between,mapping%20quality%20was%20not%20available) it is said that BWA generates MAPQ scores between 0–37.

What score should be treated as 'normal' for 30X WGS? And what is some kind of lower bound?

[serge2016]

According to https://academic.oup.com/bioinformatics/article/25/14/1754/225615, MQ > 20 is good enough:

In each batch, BWA loads the full BWA index into memory, generates the chromosomal coordinate for each occurrence, estimates the insert size distribution from read pairs with both ends mapped with mapping quality higher than 20, and then pairs them.