First, some general information about me. I am studying in an integrated bachelor's and master's program majoring in biology at a top-20 institute in India. In most aspects, my application (in my opinion) is pretty strong. I have worked in three labs at my home institution working on my own projects (i.e. hypothesis-guided research as opposed to technician-type work), and one of these projects has recently led to a preprint on which I am an author. I have been conducting my master's thesis in the US at an Ivy for the past few months. My recommendation letters will come from all profs that I have directly worked under, and I know that they will be extremely positive. Thus I know that I will handle a research environment really well and am a perfect fit for competitive schools. I will be applying to graduate programs in neuroscience in the US this year, including the program at the same uni where I am currently doing my thesis.
The reason for my worry is that I have a very average GPA. Converted to the US 4.0 scale it is 3.2, and 3.4 considering only courses from my major. My GPA has been greatly brought down by a handful of C and D grades in courses not relevant to my research interest, and overall my school has a strict no-inflation policy which has reduced my grades in courses, even those where I performed well.
Should I explain my overall low GPA in my SOP or in a separate document in my applications? My main reasons are not due to any particular hardships like health or financial issues, I was just disinterested in the courses after a few months and I spent more time in the lab than on the coursework. Would being honest about my situation as being purely self-inflicted be appreciated by admissions committees? Or should I not explain my transcript and let the rest of the application do the talking? I am mainly concerned about being filtered out at the very start (as some programs anecdotally appear to do) before my application is even read in its entirety and given a fair chance.