Hello Siddharth,
You haven't specified the name of course or entrance exam for which you are considering the qualifiying score.
But as much I know most of the courses such as engineering has the eligibility criteria over percentage of 12 th grade for PCM which is 50 percent and you must qualifiy it in order to take admission to respective course and you can't add or substitute the marks of any other subject if you don't fulfill this criterian.
Hope this helps
All the Best
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