MySQL IN Operator Not Using Index

After being alerted for elevated cpu on a staging mysql instance, I logged into the mysql console and ran a SHOW PROCESS LIST : SHOW PROCESSLIST\G *************************** 1. row *************************** Id: 1 User: my_user Host: x.x.x.x:xxx db: my_db Command: Sleep Time: 2 State: Info: NULL *************************** 2. row *************************** Id: 3 User: my_user Host: x.x.x.x:xxx db: my_db Command: Query Time: 786 State: Sending data Info: SELECT file_id, fs_file_id FROM my_data WHERE file_id IN ('123456', 123457); A query running for 786 seconds quickly caught my eye, my next course of action was to run an EXPLAIN :