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For context, I am a an undergraduate in my final semester of a US university. I am currently enrolled in five courses, so dropping the to be mentioned course would still provide me with a normal schedule.

I have just finished applying for a PhD programs in physics. While writing my applications, I was planning to take a physics course somewhat related to my field of interest (not related at all to graduating, it is a completely free slot). The semester has started, and the course is not at the level of content that I was hoping for. Hence, I am considering dropping the course. Would this negatively impact my PhD applications?

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No. Admission committees aren't deciding whether or not to admit grad students on the basis of them dropping (or completing) a single course they said they were going to take in a cover letter. Also, nobody on that committee has the time to compare classes you mention taking in a cover letter against your final transcript, and even if they did, I can't imagine a single one of them would care about the discrepancy as long as you completed your major. No need to worry about it.

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Chances are that nobody will admit a PhD student based on them having announced in their application that they will take a certain course. That would just be grossly unprofessional, as it is clear that at the point where the application is assessed, there is no evidence whatsoever that the student will know the material of the course. (Even if you take it, you could fail.)

So this shouldn't be a problem with the application. To what extent this means that you don't know certain things that you later will need when actually being a PhD student is another matter. Of course you can work through a textbook or something to make up for this if you think this makes sense.

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