MySQL slow queries - Fast using PHPMyAdmin , low CPU and RAM usage
You need to identify which queries are taking some time to execute and optimize accordingly. By default mysql does not log slow queries, so you have to add the following to your mysql config file - 

log-slow-queries
slow_query_log_file = /var/log/mysql/mysql-slow.log
long_query_time = 10     // in seconds - you can replace this with another number.


For any mysql performance issues, it is a good idea to use mysqltuner