You can reset the counter with:
ALTER TABLE tablename AUTO_INCREMENT = 1
For InnoDB you cannot set the auto_increment value lower or equal to the highest current index. (quote from ViralPatel):
Note that you cannot reset the counter to a value less than or equal
to any that have already been used. For MyISAM, if the value is less
than or equal to the maximum value currently in the AUTO_INCREMENT
column, the value is reset to the current maximum plus one. For
InnoDB, if the value is less than the current maximum value in the
column, no error occurs and the current sequence value is not changed.
See How can I reset an MySQL AutoIncrement using a MAX value from another table? on how to dynamically get an acceptable value.