Unexpected coverage across genome

Question

[Alex]

This was a sample sequenced at 10x. As you can see, the majority of the genome is covered at about 7x. This region of lower coverage comprises the assembled chromosomes of the species, whereas the region of higher coverage represents unplaced scaffolds (~700, none smaller than 10kb). I guess multiply mapped reads may be causing the issue, but I used bwa mem for the alignment and I was under the impression that multiply mapped reads are randomly assigned if an equal match occurs. Has anyone encountered this before or have a good guess as to what the issue could be?

[samuel.a.odonnell]

It is hard to say...but if I had to take a stab, often unplaced scaffolds contain a lot of repetitive material, large arrays in particular, so it could be that. The unplaced scaffolds could also be high copy number plasmids or the mitochondrial genome depending on your species and pipeline/data/etc. Goodluck

[Alex]

Thanks for the response. I agree about the repetitive material, so I tried realigning without these scaffolds but that only marginally raised the coverage (~1x). I guess for this species I may just need to request more sequencing to get the coverage I want (eg, 15x to get 10x). Although I'm still holding out hope that someone has a better solution than this...