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I've the sentence as below:

"It accounted for 90 million procedures, which is less than 90% of the total procedures..."

Can the above be changed as "It accounted for 90 million procedures, which are less than 90% of the total procedures..."?

I feel OK with the original sentence given, but going by strict rules of number agreement, the pronoun "which" (that refers to 90 million procedures, which is clearly plural) should take the verb "are." I could not find justification as to why it is correct as in the original sentence.

Any help in this regard?
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Non-restrictive which (or which after a comma, if you will) can be taken to refer back to the whole idea (a singular concept) in the preceding clause, so I believe that is is fine. Also, you're referring to the 90 million procedures as a sum, which is also a singular concept. I'd change a few other things, though.

It accounted for 90 million procedures, which is fewer than 90% of the total number of procedures.

CJ