I am not a teacher.
This is the sort of question that will probably elicit different answers from BrE and AmE speakers.
As far as I am concerned, if the percentage is of something countable then the verb is in the plural. If it's a percentage of something uncountable you use the singular.
So, 'A total of 46% of the participants were from Tokyo' but 'A total of 46% of the economy is generated in Tokyo'.
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