Hello everyone

If we have a low frequent variant (GT:GQ:DP:VF:GQX:PL:AD ==> 0/1:99:910:0.095:99:549,0,17114:824,86) (related to my previous post) and it is from DNA blood samples and I found the variant belongs in the SINE region.

We won't be surprised if the individual is found mosaic too. But should we discard variants in SINE regions? Could this low frequency in alt vs reference reads be due to repetition in SINE?

Thanks