Read coverage shows a difference in IGV

Question

[jkim]

Hello,

This is my bam file in IGV. There are way more reads mapped to the region 2 in the panel displaying reads. On the other hand, the coverage panel shows the opposite - there are more reads mapped to the region 1.

I also ran samtools depth and it said there are more reads mapped to the region 1. I am confused by this. Did IGV not show me all the reads mapped to the region 1 for some reason? I didn't change any setting for IGV.

[Pierre Lindenbaum]

may be the IGV algorithm collapsing reads generates a visual bias.

[jkim]

I see. I will post this on the IGV help forum.

[lieven.sterck]

perhaps it has something to do with the mapping quality? Image is a bit small but it seems there are much more gaps/indels/mismatches in region2 in stead of 1 ...

perhaps samtools only counts the well mapped reads or such?

[jkim]

Well, I filtered reads out in my bam by mapping quality. Yeah, I will look into samtools depth more.

[jkim]

I think I found why. If I unclick Downsampling option in alignment in preferences, it looks like IGV shows every read...

Answer 1

[GenoMax]

Check IGV preference settings for downsampling reads. Also if these are duplicate marked then check the setting for "do not show duplicates".

[jkim]

Yeah, that is why. Thanks!