Can I read "0.0012%" as "twelve thousandths of a percent" ?
"twelve thousandths of a percent" would be 0.012%
...so you are into the mouthful-area of having to say, "twelve ten thousandths of a percent" which no native speaker would dream of saying. For one thing, any listener would then spend 10 minutes working out exactly how much that was mathematically!
What a native speaker would say is
point oh oh one two of a percent- probably Americans and more mathematically-minded Britishers would say something like zero zero one two of a percent.
Do you understand what I mean by "oh oh"? (Also note that Britishers is very informal and close to slang these days)
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