Higher Coverage In Introns Than Exons?

Question

[Rubal7]

Hello All,

I have done some whole genome shotgun sequencing of Rattus norvegicus using the Illumina GA2. Looking at the mapping of reads using IGV (so not a systematic survey). I often notice a much lower number of reads in exons than in introns. Sometimes it is a striking pattern, with high coverage in introns dipping during exons and then increasing again in introns. Is there any logical reason why this might be the case? I have not heard of this phenomena before so expect it is most likely just a random pattern that would not hold up to a whole genome scan. Just thought I'd ask if anyone else has come across this before I invest more time following it up.

Best,

Rubal

Answer 1

[Stefano Berri]

you can see this related question.

The possible reason is that exon are more conserved than introns. So, the problem is when you map them. if your sequenced individual is not from the same line used for your "reference genome" then there will be miss mathces in introns and intragenomic regions that would couse more reads not to align well enough.

Alternatively, it could also be a GC content bias, but I doubt that would be visible "by eye"

[Vikas Bansal]

I think the question is other way round. There are more reads which mapped to intronic region.

Answer 2

[JC]

Introns are enriched in interspersed repeats, if you are mapping with a tool that reports multiple hits for the same read, one explanation could be that some reads are mapped to multiple repetitive regions inside (and outside) introns. You can check it if you filter your reads to keep only uniquely mapped reads and then check with IGV again.

Answer 3

[Rubal7]

If I understand correctly these explanations would explain why there is LESS coverage in intronic regions. What I observe is more coverage in intronic regions relative to exons.