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So I am doing a master's degree in mathematics in a large state school that is not very high ranked. I am planning to go for a doctorate, but not necessarily at a top school, but still an R1 school. My undergraduate degree is from Europe, and my GPA is not that great, since there was a lot of grade deflation in that school. However, it is a very good school, in top 80 on the planet.

Now, my master's GPA is quite good (3.7) right now, but the problem is: I have a B- in a core class, which is real analysis / measure theory. My previous analysis grades are pretty much all A's. I've taken other classes as well, such as algebra, number theory, topology, probability, statistics, advanced linear algebra, numerical analysis and have pretty much all A's in those. My question is: how much would this one B- affect my chances of admission?

Szemeredi_31
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Since I am frequently a member on the PhD student admission committee in our math department, I can tell that B- in one class does not really affect the chances. What affects it are recommendation letters and Summer projects (REUs).

If the letters are not very strong and there was no (Summer) research done, the chances at my department are very small.