Comments (15)
I can't reproduce this, and its not really possible to guess what is going on from the screenshots.
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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.
from igv.
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.
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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.
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Related Issues (20)
- Reverse 5' to 3' display HOT 5
- How to Increase the Font Size of Numerical Data Displayed in Tracks HOT 2
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- Desktop app downloads page links not working: 503 Service Unavailable HOT 2
- Setting track color doesn't work for splice junction tracks
- BigWig Performance Regression HOT 19
- Inquiry About Overlaying .bed and .narrowPeak Files in IGV HOT 8
- Gencode genome no data HOT 1
- Custom URI support for IGV application. HOT 1
- group by haplotype? HOT 4
- question about colors of alignments HOT 1
- Quantifying DNA Methylation on Bisulfite Mode (comparing two) HOT 3
- Troubles launch IGV on windows HOT 7
- IGV for Windows: Add Install/Uninstall data to "Programs and Features" and Registry
- Sashimi Plot Supporting Counts Label Visibility when Zoomed In
- IGV quits unexpectedly when saving tracks HOT 3
- IGV config JSON schema HOT 1
- Download fails with "Virus scan failed" error HOT 1
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