What are typical unmapped and unintegrated fractions

Microbial community profiling HUMAnN
1

Hi

I would appreciate if you let me know if I am getting “normal” mapped and integrated fractions or not.

Using humann v3.8, UniRef90 and default settings, on human gut microbiome (in humanized mice), illumina shotgun (length 150) metagenome.

Reads mapped = 76.1 - 86.1%
Reads integrated = 4.1 - 5.7%

Are these fractions normal or too low?

Thanks

Gurjit

2

Those look very normal. In fact 75-85% read mapping is quite good. The vast majority of genes are not annotated to known metabolic pathways, which is why the integrated fraction (i.e. reads assigned to pathways) is low. Given that 5-10% of proteins are assigned to ECs, not all of which are incorporated into pathways, 5% integration strikes me as reasonable.

1 Like