Interpretation issue

[esthernmolina]

Hi,

I'm trying to analyse some cases using REViewer included in STRipy pipeline. In the analysis of one of the cases I'm working on, specifically with the RFC1-AAGGG gene, I can see vertical black lines in the aligned reads when mapped to the reference genome, as you can see in the attached image. I'm unable to understand the meaning of these lines, and I could not find any information about them in the REViewer documentation.

Could you please help me with this interpretation? Thanks.

[sclamons]

It's been a while since I've actually used these, so you should check that this makes sense, but as I recall the vertical black lines are insertions relative to the reference. Based on the rest of your reads, I'd guess you have more "AAAGGG" repeats than "AAGGG".