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To calculate percentage in 12th board for filling jee mains application form you need to consider the marks scored in five subjects - (1) Physics, (2) Chemistry, (3) Mathematics, (4) A language and (5) Any subject other than the above four, is taken into account. So, it's good that you don't replaced chemistry marks by cs marks. Also, you don't need to worry at all, you will not face any problem as there's no percentage barrier to be eligible for jee mains. The criteria to be eligible for jee mains is that candidate should have passed class 12 or qualifying the exam in 2018 or 2019 or should be appearing in 2020 for it with Physics,Mathematics, and any one of (Chemistry, Biology, Biotechnology, Technical Vocational Subject).

The percentage barrier comes while taking admission in NIT,IIT and GFTI for which candidates should have obtained a minimum of 75% marks in class 12 or equivalent exam or they must be in the top 20 percentile in their class 12 examination. For SC/ ST, the eligibility is to obtain a minimum of 65% marks in class 12 or equivalent.

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