Hey!

IIT-JAM examination's result is in no way related to your Bachelor's marks. Although, it might affect your admission in certain institutes.
In IITs, the admission in MSc courses is solely based on your IIT JAM ranking. In institutes like IISERs and IISc, the shortlisting is done on the basis of IIT-JAM ranking, your BSc marks, your statement of purpose, etc. You will be called for interview. Final selection will be based on combined result of every applicant.

Hope it helps!

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