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Under some conditions the extended barrel will do more damage even against armored opponents! I did some calculations so the decision will be easy. This is based on level V mods in singleplayer; General trend is that high damage weapons like the barrel better.
Death Durron posted... What is defined as armoured opponents? Enemies with Armour "health" such as Brutes and Banshees? Do all of Cerberus troops count as having armour or only the Guardians and their shields?
Just plain "armor" like brutes. Shields and barriers are damaged the same as health, and guardian shields are physical obstacles.
Armor has a flat damage reduction on a per bullet basis. That's why high damage weapons don't benefit from armor penetration mods very much.
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