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?