How do I diagnose missing rows on a MySQL slave? I'm running traditional master/slave replication on MySQL 5.1.52, my master is set for statement based replication.  A few tables are missing rows on the slave (differing row counts), these tables are insert only on the master using "load data infile ...", with auto-increment Pks.  It is strange that the missing rows on the slave have gaps in the PK values where the rows should be.  Slave is marked read-only so there are no accidental deletes.
The traditional way would be to use pt-table-checksum and pt-table-sync

I like doing things a little different. I immediately run pt-table-sync with the --sync-to-master --print options.

Here is the --sync-to-master option


  --sync-to-master
  
  Treat the DSN as a slave and sync it to its master.
  
  Treat the server you specified as a slave. Inspect SHOW SLAVE STATUS,
  connect to the server’s master, and treat the master as the source and
  the slave as the destination. Causes changes to be made on the master.
  Sets --wait to 60 by default, sets --lock to 1 by default, and
  disables --[no]transaction by default. See also --replicate, which
  changes this option’s behavior.


Here is the --print option


  --print 
  
  Print queries that will resolve differences.
  
  If you don’t trust pt-table-sync, or just want to see what it will do, this is a good way to be safe. These queries are valid SQL and you can run them yourself if you want to sync the tables manually.


This, if you do something like this:

echo "SET SQL_LOG_BIN=0;" &gt; /root/SQLChanges.sql
pt-table-sync --print --sync-to-master h=10.1.2.30,u=username,p=password &gt;&gt; /root/SQLChanges.sql


The file /root/SQLChanges.sql will contain every change you need to execute on the Slave. Once you are satisfied with its contents, just execute the script on the Slave.

With regard to using LOAD DATA INFILE in Replication, @DTest answered this question about that. I further explained how mysql replicates LOAD DATA INFILE.