Actually only very few are from vaults. Only a hand full of Vaults were specifically built for protection against nuclear fallout. Most were experiment conducted by Vault Tech. This is were Super mutants come from and why most of the vaults you explore have so much -blam!-ed up shit in them.
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Edited by Roadkii J: 7/26/2015 8:13:25 AMWell... Where the east coast Super Mutants came from anyway... Unless your counting Mariposa as a vault?