slow log contains query, but query time is less than long_query_time mysql&gt; select @@long_query_time;
+-------------------+
| @@long_query_time |
+-------------------+
|          2.000000 |
+-------------------+
1 row in set (0.00 sec)

mysql&gt; select @@log_queries_not_using_indexes
    -&gt; ;
+---------------------------------+
| @@log_queries_not_using_indexes |
+---------------------------------+
|                               0 |
+---------------------------------+
1 row in set (0.00 sec)


but the slow query log contains:

# Query_time: 1.000111  Lock_time: 0.000000 Rows_sent: 1  Rows_examined: 0 SET timestamp=1559116596; select sleep(1);


Is there any other variable that affects this?
If you add to my.cnf ( or my.ini )

min_examined_row_limit=1

the line should be omitted in the slow query log - in this case, no rows were examined.