Translocation in IGV

[tahamasoodi]

Hi,

I've sorted alignment in IGV by Insert size and accoeding to IGV if there is red color that means there is a deletion. Now from the screenshot attached, does it indicate there is deletions between these two locations? If there is a deletion, then there should be no reads in between these two breakpoints. Can anybody through light on it?

Thanks,

[dpryan]

Presuming this is a diploid organism, I would expect you have a deletion on one of the chromosomes. That wouldn't preclude reads mapping to that section of the other copy. Alternatively, I could imagine such a result occurring around repeats, though I don't know if that would ever occur in reality. You might get a better idea whether this is real or due to a sequencing/alignment artifact by zooming in on some of the breakpoints and seeing if this might, indeed, be due to something non-interesting.

If this is real, then it's taking out the start of a gene, which I imagine could be quite relevant to whatever you're working on.

[tahamasoodi]

Thanks dpryan! How does zooming help to detect sequencing/alignment artifact? What start of the gene has to do with it?