How you earn weapons usually defines it's color. At least in my experience. All weapons I get from Crucible matches (not Engrams) seem to be red while story weapons have been coming in blue. The gunsmith offers goldish and grey and the Vanguard guy has white.
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You're right. I do have a legendary sniper Final Boss that is burnt orange and shades of grey and black. Awesum handling weapon. Comes in all 3 element flavors if you can find em all.
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I need a legendary sniper lol. All I've gotten are rares.