insertions and deletions in IGV

[c c]

Hello

I am using IGV version 2.11.9.

I understood that deletions are not included in the total count.  Are insertions included?

(example attached)  Is total count 4929 to include deletions or is it 5591 to included deletions and insertion reads?

deletion 19% (938/4929)

insertion 13% (662/4929)

Thank you

Total count 3991

A: 1 (0%)

C: 3949 (99%)

G: 0

T: 0

N:41 (1%)

----------

DEL: 938

INS: 662

[igv-help]

All the numbers are there in the popup, there is nothing hidden.  3,949 reads have "C" in the read sequence at that location, 1 has "A", 41 have "N", and 938 have a gap (deletion).    So there are 3,991 + 938 = 4,929 reads spanning that locations.   Insertions are special because they are really between locations, or to one side so-to-speak, by definition they do not have any genomic location.   So it would be incorrect to add the insertions to the total pileup.     Put another way, imagine a single read with an "A" at a location, and an insertion adjacent.   You would not have 2 reads spanning the location, only 1.

[c c]

Thank you for the very clear explanation!

Cheers

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/3d047665-056f-432e-99db-ac9f38f1c8c6n%40googlegroups.com.

[James Robinson]

Hi,  what exactly is your question?  

On Wed, Feb 26, 2025 at 6:18 AM sania Rauf <rauf.s...@gmail.com> wrote:

This is info on my excel sheet chr num, start  end   reference  alt
12   6711145    6711147    TCC    -
But when i look into IGV there is different thing, plz help in this