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Your site’s keys, at any rate for the WordPress core tables, are the ones created by this plugin.
The columns you mentioned don’t have keys. It’s very rare that all columns in a table have keys; they don’t help performance unless they’re used to search the table..
According to your uploaded metadata, your site is provisioned ok. But the metadata doesn’t show information about your site’s stack other than your dbms. So I don’t have enough information to explain