I have generated tophat alignment from RNAseq data with default settings. When I visualize the alignment on Golden Helix genome browse, 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 position 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 coding region 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!