Difference between mapping quality and minimum base quality

Question

[A_heath]

Hi all,

I am using Freebayes for haploid variant detection and I do not get the difference between parameters -m (mapping quality) and -q (minimum base quality). Could you help me, please?

Many thanks for your much appreciated help!

Answer 1

[dthorbur]

Mapping quality (MAPQ) refers to probability that the mapping position is wrong. Base quality refers the score given to each nucleotide by the sequencing platform, and is an estimated probability of the base being incorrect. MAPQ takes base quality into account.

[A_heath]

Thank you for your reply dthorbur!