Dear all,

is it possible to visualize insertions in a sequence?

I have prepared a simulated sequence of the mitochondrial genome from the release hg38 by placing non human sequences right in the middle of it (position 8284). I then aligned the simulated genome to the mitochondrial index and the visualized the alignment with the integrated genome viewer IGV. However, I don't see any sign of insertions in the figure.

![enter image description here][1]

Is there a way to highlight the insertion point? Maybe by showing only clipped reads or the reads that map only on one mate?

Thank you.


  [1]: http://u.cubeupload.com/gigux/Msplitpoint.png
I see evidence of the "transgene" insertion: all those **identical soft-clipped bases** centered at the position you inserted the non-human sequence. Pay attention: 1) all reads are soft-clipped at the same reference position, 2) as far as I can tell, all soft-clipped bases are identical between different reads.

Look at the picture below. The big red arrow indicates the insertion point, and the darkened rectangles indicate the inserted sequence (which I was able to determine as parvovirus by blasting them, even before you told us it was parvovirus).

<a href="https://ibb.co/eSbiRK"><img src="https://preview.ibb.co/gzBHmK/image3721.png" alt="image3721" border="0"></a>

However, keep in mind this visual inspection works well because you have a simple, small and with no duplications reference genome, and a simple and small insertion, without other copies of it throughout the reference genome. As WouterDeCoster [pointed above][1], there are better methods to identify structural variation events in more complex scenarios.


  [1]: https://www.biostars.org/p/331663/#331694