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If you frequently delete rows (or update rows with variable-length data types), you can end up with a lot of wasted space in your data file(s), similar to filesystem fragmentation.
Sometimes you find yourself in a bad situation where your only hope of recovering your InnoDB data lies in a handful of .frm and .ibd data files that were heretofore part of a working MySQL installation.
If you’re using MySQL replication, chances are your master and slave databases aren’t entirely consistent. There are a number of reasons for this. Some MySQL functions like UUID() don’t replicate properly with statement-based replication.