Hello aspirant,
The national testing agency only considers the marks of your class higher secondary or equivalent examination for the eligibility criteria. So, even if you have completed your M.Sc , ypour qualifying examination will still be your class 12 examination and not your B.Sc or M.Sc result. If you belong to the General category you need to have a 50% aggregate in your class 12 examination for being eligible else you need to have 45% aggregate. All the best!