Interpret IGV

Question

[najim3]

Hello, Biostars community.

Does anybody know the genetic event that results in the reads' alignment in the example below? Note the green reads, which usually support the breakpoints for a tandem duplication, whereas the red reads indicate reads that bridge a deletion. Note also that the coverage remains comparable to the up- and downstream region. Thanks

Answer 1

[benformatics]

What is the sequence in the region of the break point? How long are these reads - that is probably the key?

You have 4 reads supporting a tandem duplication with your ~50-100X coverage that's insufficient in my book.

[najim3]

The read length is 150 nt. I agree that there are few reads supporting a "tandem duplication" and a "deletion". However, I have observed several genuine SV events supported by even less reads. Several other samples do NOT show these aberrant reads. The sequences at the breakpoints are probably relevant (as they are for most structural variant events).

Here is an updated screenshot where the sample is compared to an independent case.