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There are various framework-specific tools for db query profiling on the client side, I guess it depends on the stack that your app uses. On the server side I suggest to use pt-query-digest from Percona Toolkit.
Not a waterfall, phpmyadmin has a reasonably pretty pie chart
Otherwise,
https://dev.mysql.com/doc/refman/5.5/en/show-profile.html
and you're able to log 'slow queries'
https://dev.mysql.com/doc/refman/5.7/en/slow-query-log.html