Hello,
Your percentile in JEE Mains is used to calculate your rank in JEE Mains. If you are from a particular reservation category, then your category rank is also calculated using your percentile score.
Your percentile score represent the percentage of students who have scored less than you in JEE Mains. For tie breaker, various other factors are also considered for rank calculation
The JOSAA counseling is done on the basis of your rank in JEE Mains. For the reservation category, they are alloted seats based on their reservation category list.
JOSAA counseling is done for admission into various engineering and architecture courses into the various government engineering colleges in India like NITs IIITs and GFTIs.
Please visit this link to know more details about JOSAA counseling
Hope it helps

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