Turn on the slow query log so Zynty can surface the queries actually costing you performance.
A threshold of 1 second is a reasonable starting point, tune it down once you've cleared the obvious offenders.
SET GLOBAL slow_query_log = 'ON'; SET GLOBAL long_query_time = 1; SET GLOBAL log_output = 'TABLE';
GLOBAL variables reset on restart unless they're also set in the config file.
# my.cnf [mysqld] slow_query_log = 1 long_query_time = 1 log_output = TABLE
The database's Overview tab lists the slowest queries in the current window, with average duration and call count, so you can prioritize by actual impact rather than guesswork.