90%, 99%, 99.9%…effective translate into 10%, 1%, 0.1% ineffective. Or in exponential notation, 10^(-1), 10^(-2), 10^(-3), etc.
It’s just an easy number. “99.9% effective against bacteria” means that 1 in 1000 survives. 98.9% would mean that 1 in 90.9 survives. One of these reads nicer than the other.
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