Which MySQL shows CPU usage? I am monitoring MySQL server using phpMyAdmin [Status => Monitor] function. And it shows a number of useful graphs. 



Which variables (or which mechanism) is phpMyAdmin using to pull this data? 

ps. I was wondering if it is calling SHOW STATUS query?   But when I look through a bunch of variables resulting from SHOW STATUS I cannot spot anything related neither to CPU, memory or not even active connnections...
Some guesses.  Some things come from SHOW GLOBAL STATUS (highlighted and with initial caps, below); some from elsewhere.

Questions:  Status Questions or Queries.  The latter seems to include statements inside Stored routines.

Connections:  Not Connections since that continues to grow.  Probably not Threads_running since that should be very small.

Processes:  Perhaps from the OS.  Are you using Windows?

Traffic:  Bytes_sent/received.  (Not very useful)

CPU Usage:  The OS.  That is high.  You have some slow queries and/or poor indexing.  See the slowlog (more below).

System Memory:  The OS.  See top or whatever Windows has.  Sounds like there is room to increase some settings.  Do you have 6MB of RAM?

Swap:  From the OS.  No swapping is Good.

Slow queries:  Slow_queries.  0 is good ...IF... you have a reasonable value for long_query_time, which defaults to 10 seconds.  Change it to 1.

Key reads:  Maybe Key_reads, which applies only to MyISAM.  Are you using that engine?  Maybe Handler_read_key, which applies to all engines, but is not useful by itself.

The graphs are pretty, but mostly useless.

I may be able to give you about 20 tips from the full set of VARIABLES and GLOBAL STATUS, plus tips from the slowlog, once you make use of it:  http://mysql.rjweb.org/doc.php/mysql_analysis