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I've been advised by Glyph when new upgrades arrive at the terminal in Liara's room and thus far each has offered a choice of two benefits that I have to choose between.

What are the upgrades that are available? Do they transfer in NG+ so that I could theoretically double up on the bonus or pick the other option?

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They do Transfer in a new game +. –  LessPop_MoreFizz Mar 13 '12 at 14:59
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They are mostly just +5% to things like damage, powers, cool down, health, shields, ext. There is one for store discounts and another to heal your scars if you didn't do that already in ME2. You are always given a choice between two, but you can get the same upgrade twice.

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