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?