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You deal 25% more damage with silenced weapons. Stealth is also increased in shadows to 10% less visibility, equivalent to half the effect per rank of the Sneak perk.
As it is a percentage damage bonus, the order in which it is acquired has no effect on the Cloak & Dagger > Ninja 3 > Mister Sandman 3 damage multiplier calculation. It can be earned at any time with no change to the final damage bonuses.
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