Sudden coverage increase in IGV

Question

[mrs97]

Hello, I was wondering if anyone knows how to interpret this sudden change in coverage in IGV? I've aligned illumin reads of the system against the pacbio generated genome. In the vast majority of this genome, the coverage from one base to the next increases in a gradual manner so the coverage track looks more like a wave, but here it's a much more sudden jump, almost to twice the coverage of the surrounding bases. Does this mean that the region of increased coverage is representing two alleles while the lower coverage area is only representing one? Any ideas about this would be greatly appreciated!

[Pierre Lindenbaum]

it looks like a small duplication.

Answer 1

[GenomeXP]

As Pierre just wrote, it looks like the sample you sequenced has two sequences like this one in it's genome, and your reference genome only has one such sequence. So your mapping software stacked the two alleles on top of another giving you twice as many reads there.