Hi,

I have generated tophat alignment from RNAseq data with default settings. When I visualize the alignment using IGV or Golden Helix genome browser, I notice these light grey stacked pile of reads labeled as "intronic depth". These seem to typically map over intronic regions and have a good coverage but I can't see the base or any other information related to it. For instance, I have a site in the mapped alignment happen to be in a coding gene exonic region marked with:

match        G     2 reads
mismatch     A     20 reads
intronic           150 reads

Does anyone know what does this "intronic depth" means? How can I explain these intronic reads in a site where I see a somatic change? are these of concern? should such site with a variant be considered as genuine?

I would appreciate any feedback or help. Thank you!

BD