The MySQL/MariaDB optimiser likes to know things like the cardinality of an index – that is, the number of distinct values the index holds. For a PRIMARY KEY, which only has unique values, the number is the same as the number of rows.  For an indexed column that is boolean (such as yes/no) the cardinality would be 2.

There’s more to it than that, but the point is that the optimiser needs some statistics from indexes in order to try and make somewhat sane decisions about which index to use for a particular query. The statistics also need to be updated when a significant number of rows have been added, deleted, or modified.

In MyISAM, ANALYZE TABLE does a tablescan where everything is tallied, and the index stats are updated. InnoDB, on the other hand, has always done “index dives”, looking at a small sample and deriving from that. That can be ok as a methodology, but unfortunately the history is awkward. The …