Hello Shubham,

Based on the information provided by you above in the question, it is really hard to say on what basis you should aply for admission. However, the JEE score is more valuable than the boards' percentage, so you should go for the JEE score. Also, only consider the boards' score only in non engineering courses, for any engineering course if there is an option you shuould always opt for the JEE score, untill and unless your score is too low. All the Best!