Abnormaly amount of reads

Mr.Zurich1992 · 10-01-2016, 01:42 PM

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 · 10-02-2016, 03:44 AM

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).

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10-01-2016, 01:42 PM	#1
Mr.Zurich1992 Member Location: Switzerland Join Date: May 2013 Posts: 20	Abnormaly amount of reads 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?

10-02-2016, 03:44 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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).