Variants outside genes

[Marie_Noir]

Dear all,

not sure if this is the best fitting place for my question, but since it arose during bioinformatic analysis of my NGS data, I will post it here.

I realized that although I have data from EXOME sequencing (enrichment with a standard kit from, I have to look it up, either Agilent or Nimblegen), I encountered lots of variants OUT OF known genes (as mapped onto NCBI genes, build 37). I know, that enrichtment is not 100% perfect, but I want to know what percentage of "extragenic" enrichtment is "normal"? I would be happy to hear about your experiences.

Thanks in advance!

[swbarnes2]

Dear all,

not sure if this is the best fitting place for my question, but since it arose during bioinformatic analysis of my NGS data, I will post it here.

I realized that although I have data from EXOME sequencing (enrichment with a standard kit from, I have to look it up, either Agilent or Nimblegen), I encountered lots of variants OUT OF known genes (as mapped onto NCBI genes, build 37). I know, that enrichtment is not 100% perfect, but I want to know what percentage of "extragenic" enrichtment is "normal"? I would be happy to hear about your experiences.

Thanks in advance!

The companies making the kits usually promise about 60% on target. Once I got 70%. So yeah, expect a lot of off target reads.