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I have 3,066,691 queries logged and some red numbers in my phpmyadmin status information:
There are also green numbers in phpmyadmin but I don’t know what they mean ? I use Typo3 and MySQL.
The MySQL Tunin Primer Script was helpfull for me. It gives some helpfull hints and shows which values are good, which one bad.
For TYPO3 i guess, some slow_queries are no problem, the will probably occur only in the backend.