Interpretting IGV output

Question

[analyst]

Hi all,

Please help me interpreting blank white spaces between pairs (insert). Is it showing deletion? And why is there only one red colored pair while others are grey.

Thanks

Answer 1

[Carlo Yague]

1. About the white space (inner distance)

The white space between the reads of a pair is called the inner distance, not the insert. The insert is composed of both reads + the inner distance. Contrary to the reads, the inner distance has not been sequenced, so its length and sequence can only be inferred based on the alignment of the read pair.

2. About the read color code

The colors of the reads is explained in the documentation: https://igv.org/doc/desktop/#UserGuide/tracks/alignments/paired_end_alignments/ By the default, when the inferred insert size of a pair is larger than expected, both reads are colored in red. This might be something different in your case since the red pair doesn't appear to have a much larger insert size than the other reads. You can easily verify that by clicking on the read and reading the information providing by IGV.

[analyst]

Thanks Carlo!

And what does this 4 represent. Is it 4 bases deletion?

[Carlo Yague]

Yes, it is: https://igv.org/doc/desktop/#UserGuide/tracks/alignments/viewing_alignments_basics/#indels