What do solid red/green reads in IGV mean (looking at SARS-CoV-2 BAM)

Question

[Cornelius]

I'm looking at a SARS-CoV-2 BAM for the first time - in IGV.

I understand how I can spot SNPs and deletions, but especially at the terminals of the genome, there are entirely solid green reads, and a lot of them.

I googled but can't figure out what they mean. Would be nice if someone could explain to me, thanks!

Does this mean there alternative regions where this read could align? Is this of any use for SARS-CoV-2 bams?

Answer 1

[Istvan Albert]

Right-click on the alignment and visit the option "Color alignments by" it will tell you what option is selected.

Also, right-click and select "View as pairs", it usually becomes evident why things are colored certain way.

I am guessing you have Color by insert-size and pair orientation selected, the green indicates alignments that go tail-to-tail and the red are alignments that are longer than expected.