Bug in showing mismatched bases about igv

[jrobinso]

I can't reproduce this, and its not really possible to guess what is going on from the screenshots.

[gevro]

Weird, I tried to reproduce it and can't. There was something in that specific read that was preventing it from showing mismatches. Unless there is some setting in preferences that can somehow cause mismatches not to show up even when 'show mismatched bases' is selected.

[jrobinso]

I can't think of any setting that would cause that, if its low base quality changing the shading formula in preferences might but I doubt it. Are you sure you are looking at the same alignment? Its impossible to say from a screenshot, alignment rows might be in a different order between the two.

[gevro]

100% sure I was looking at the same alignment. And I turned off shading by base quality - I thought of that - and no difference.

In that session of IGV, for some reason for that specific alignment, the mismatches were not showing up per the screenshot. The screenshot for sure shows that so I know I'm not hallucinating :-) And going to other loci in that session showed mismatches fine.

If it recurs, I will let you know.