why are the term_id and term_taxonomy_id doesn’t match on custom taxonomies, but are duplicates on categories

  1. term_id is a unique ID for the term.
  2. term_taxonomy_id is a unique ID for the term+taxonomy pair.

A taxonomy consists of sometimes many terms, so basically the term_taxonomy_id links the term_id to the taxonomy.

All info on these can be found here:

http://codex.wordpress.org/WordPress_Taxonomy

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