Quality of Mapping using bwa flagstat

Question

[BeetleCheers]

Hi there, I am mapping single-end reads to a draft reference genome using BWA. The workflow I was given says that a 90% map is good, but does not have anymore information than that. The example flagstat output is given as something like this (i've truncated it for easier reading):

1182945 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 secondary

2498 + 0 supplementary

0 + 0 duplicates

1093076 + 0 mapped (92.40% : N/A)

However, I get a huge range in percent mapped (eg: up to almost 100% and way down to 0.6%). Is there information about expected % mapping? I'm using draft genomes that are known to have some mistakes, so can I lower this acceptability threshold down to say 80%?

[swbarnes2]

What 'goodness" are you trying to measure here? A low mapping % might mean a poor quality run, or it might mean your reference genome doesn't match your sample.