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The percentages given are "user", which means the time the CPU spends running userland programs, "system" which is the time spent doing kernel tasks, "nice" which is the time spent doing tasks with a nice value of less than 0, and idle time.
"niced" tasks have to execute at some stage in either user or kernel space, so therefore the overall total you see will be more than 100% if there are many niced programs running.
It's the user CPU you're seeing the 44%, not overall. So that would mean for that user, MySQL is taking 44% of what the user is using, which may be .01% of the system as a whole. Does that make sense?