I am seeing C to T transitions in my sequencing data, but also some strange signatures that follow along with that. I am trying to understand the biology of what is occurring. In the data I see more C to T changes than G to A changes, when it would be expected that these numbers would be relatively the same.
So, in vivo when a C to T transition occurs, does the complementary base get changed to ensure watson and crick binding, or will you end up with a T-G pair? This would explain the phenomenon that I am seeing but I don't know if this happens. (Andy references would also be super helpful. Thanks.)