what does total count mean at a location in IGV

Question

[newDarkAB09834]

Hi All,

In a BAM file when loaded in IGV and then when clicked on a location (eg: 27792) it shows that the Total reads at that location is 27 and DEL 215.

But in that location it can be seen more than 27 reads if you count the gray reads. And less number of deletions if you cont the black-lines in that location.

So my question is what does the Total count= 27 mean in that location ?

Thank you.

[cmdcolin]

to me, it looks like it could be a bug but I couldn't say, it seems to think there are 215 deletions operations (presumably from CIGAR string) crossing this position but that isn't evident from your screenshot

[newDarkAB09834]

Actually there are not that many deletions if you look in the IGV. Let me try to upload a new image to make it clear.

[newDarkAB09834]

A new image of the deletions. These are all the deletions which can be seen in the IGV. (black lines represent the deletions)

1. So clearly there are not 215 Deletions according to the image. Can you confirm what DEL 215 mean ?

1. As it says Total Count = 27 The image clearlly shows that there are more than 27 reads. So what does Total Count=27 mean ?