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Hello Ashish,
12th boardd percentage is calculated on the basis of all the subjects taken by you in Class 12th. I don't think there are only four subjects as in CBSE and most other boards too, it is the aggregate of five subjects you opt for in class 12th. Five subjects are a minimum requirement. In some cases, people opt for one extra subject and call it the sixth subject which is optional. JEE requires a minimum of 75 percentage for admission in IIT which must include Physics, Chemistry and Mathematics subjects.
Hope this helps!
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