Entering edit mode
6 months ago
Daniel
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0
Hello all,
we are currently not quite sure what we see here. All three are directly related to each other.
Now we are wondering why the coverage across all 3 genomes is so poor, also we see a startloss in CTBP1 which is known for defects in the respiratory chain. This would fit.
We are currently not quite sure whether we should take the startloss seriously due to the low coverage. But it also makes us wonder why the coverage across the three files is so low at this point.
How would the professionals proceed here? Has anyone seen this before or have an explanation?
you could try to plot "view as pairs" to see if there are reads that are paired across this gap of "low coverage". there are definitely other reasons that there might be low coverage besides a deletion, but long distance read pairing would lend evidence to a true deletion SV. I tried loading up some random bam files like HG002 bam files and plotting mappability in this region and the coverage from HG002 was fine and mappability also looked good. the only thing that looked a bit interesting is that GC content in this region is up to ~80% but i don't really know how that influences sequencing
note that the view as pairs may not confirm the "start loss" that appeared in the low coverage reads, but might explain the overall coverage drop
Here is a screenshot with Read as Pairs.
Did I understand correctly that a startloss can lead to the coverage being regressive in this position? How is this to be explained technically? We have already thought about LongReads. Would that bring more light into the darkness here?
Daniel why did you delete this post?