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%?