dear aspirant,hope you are doing well.now coming to your question,the seats that are left in 2nd councelling is converted to all india quota seats.These seats will not be filled by MCI in 2nd round;but these seats will be filled by MOP UP round that is going to take place soon.
hope this will help.
please do check:http://learn.careers360.com/careers360-talent-search-exam.
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