if you want to keep the row with the lowest id value:
DELETE n1 FROM table n1, table n2 WHERE n1.id > n2.id AND n1.meta_key = n2.meta_key
OR if you want to keep the row with the highest id value:
DELETE n1 FROM table n1, table n2 WHERE n1.id < n2.id AND n1.meta_key= n2.meta_key
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