igv different width on reference gene exon

Question

[Nich]

Hey guys I used igv to check a WES bam file. When I looked to EGFR gene, I saw that the refseq genes with blue thicker bar had a better coverage of reads. However there is little read on the blue thinner bar region.

I thought all blue bar region was exon. Now I don't know whether I am right.

So, the question is: 1, Does the whole blue bar mean exon region? What the exact mean of thicker bar and thinner bar？ 2，Why the blue thicker bar has a better coverage ？Please help me find some possible reasons.

Thanks everyone！

[Nich]

I don't know why the pic can not display well ………… I share the pic on a pic website

https://freeimage.host/i/21SeTu

[GenoMax]

Follow the instructions here : How to add images to a Biostars post

Answer 1

[Jorge Amigo]

RefSeq track on IGV shows all gene information available, and the coding region is represented thicker.

If you open a WES bam file on IGV you should see coverage islands on top of all WES probes, and these WES probes should be designed on top of all coding exons. You can load the design bedfile on IGV to see that too.

And that's why you should see your bam file's coverage islands on top of RefSeq's thicker regions.