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How MySQL ‘queries’ and ‘questions’ are measured
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MySQL has status variables “questions” and “queries” which are rather close but also a bit different, making it confusing for many people. The manual describing it might not be very easy to understand:

Queries
The number of statements executed by the server. This variable includes statements executed within stored programs, unlike the Questions variable. It does not count COM_PING or COM_STATISTICS commands.
 Questions
The number of statements executed by the server. This includes only statements sent to the server by clients and not statements executed within stored programs, unlike the Queries variable. This variable does not count COM_PING, COM_STATISTICS, COM_STMT_PREPARE, COM_STMT_CLOSE, or COM_STMT_RESET
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