Strange pattern of uneven read count distribution

Question

[BioStar22]

Hi Biostars,

I have multiple murine whole genome sequencing samples which show a non-uniform readcount distribution along the genome, all following the same pattern, example attached. Has anyone be facing this pattern in readcount distribution before and may have an idea what could be causative? (i dont see patterns in standard QC parameters)

Thanks for any input on this!

Answer 1

[shelkmike]

Sequencing coverage by short reads depends on GC content (https://pubmed.ncbi.nlm.nih.gov/22323520/). Maybe, this coverage distribution reflects distribution of GC content along chromosomes?

Also, if you removed reads with low mapping quality, this may have reduced coverage in repetitive regions.