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I am using IGV to view the mapped bam file to the reference- some genes have no coverage at all (no grey bars)- how could I know if these regions are absent from my genome (compared to the reference) or they were not sequenced at all?
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You are not going to know for sure from data you have at hand. Here are a couple things to consider.
If you have good coverage on either side of the region you are not seeing then there is a chance that the region is absent in your genome (you will need to verify by additional experimentation).
If you do not have uniformly good depth of coverage across the genome then you would not know if a particular region was not sequenced. You would probably need to sequence deeper in that case. -
Igv
Yes- this makes senseOriginally posted by GenoMax View Post
I was wondering why I can see in IGV white bars at certain regions (not grey bars)?Comment
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Their MAPQ is 0 (otherwise, they're grey or another color).Comment
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Is this exome capture? If so I would check the regions are captured by the kit used in the first place. The bed files for the capture regions will be available from the manufacturer, and it may be that the regions might not be sequenced for this reason.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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