Abnormaly amount of reads

[Mr.Zurich1992]

I have sequenced my genome with depth 10x. When i use IGV, I can see on chromosome 5 a small sequence where it shows a very high amount of reads like over 2000 reads!!! thats crazy. Why that? My mother also has this.

What kind of SV could this be?

[dpryan]

It could be a copy number variation, but more likely it's rRNA or some other region that's just not correct in the reference genome (i.e., it might not be a variation at all).