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So my senior year the only way I could take this course was if I registered for it under "readings & research" instead of the actual course title. I ended up asking my professor for a LOR and I'm positive he wrote that I was his student under the actual course title but if you look at my transcript it doesn't show that I ever took such a course. Do I need to write an explanation of some sort? I'm not sure what to do.

This is something outside of your control and not something you need to do anything about or even worry about.

I don't think anyone in admissions looks that closely. I'd be interested in how long they even spend on app. Maybe 5 minutes total?

Thank you both! I hadn't even thought of it being an issue but got nervous just as I was about to submit. But you're right, it is what it is and I doubt it's that important.