log_slow_queries = /var/log/mysql/mysql-slow.log
long_query_time = 2
log-queries-not-using-indexes

explain low_query

SELECT t.TABLE_SCHEMA AS `db`,
t.TABLE_NAME AS `table`,
s.INDEX_NAME AS `index name`,
s.COLUMN_NAME AS `FIELD name`,
s.SEQ_IN_INDEX `seq IN index`,
s2.max_columns AS `# cols`,
s.CARDINALITY AS `card`,
t.TABLE_ROWS AS `est rows`,
ROUND(((s.CARDINALITY / IFNULL(t.TABLE_ROWS, 0.01)) * 100), 2) AS `sel %`
FROM INFORMATION_SCHEMA.STATISTICS s
INNER JOIN INFORMATION_SCHEMA.TABLES t ON s.TABLE_SCHEMA = t.TABLE_SCHEMA AND s.TABLE_NAME = t.TABLE_NAME
INNER JOIN (
SELECT TABLE_SCHEMA, TABLE_NAME, INDEX_NAME, MAX(SEQ_IN_INDEX) AS max_columns
FROM INFORMATION_SCHEMA.STATISTICS
WHERE TABLE_SCHEMA != 'mysql' GROUP BY TABLE_SCHEMA, TABLE_NAME, INDEX_NAME ) AS s2 ON s.TABLE_SCHEMA = s2.TABLE_SCHEMA AND s.TABLE_NAME = s2.TABLE_NAME AND s.INDEX_NAME = s2.INDEX_NAME
WHERE t.TABLE_SCHEMA != 'mysql' /* Filter out the mysql system DB */
AND t.TABLE_ROWS > 10 /* Only tables with some rows */
AND s.CARDINALITY IS NOT NULL /* Need at least one non-NULL value in the field */
AND (s.CARDINALITY / IFNULL(t.TABLE_ROWS, 0.01)) < 1.00 /* unique indexes are perfect anyway */
ORDER BY `sel %`, s.TABLE_SCHEMA, s.TABLE_NAME /* DESC for best non-unique indexes */
LIMIT 10;