It's a function of how much a player contributes to his team on both ends of the court. This effectively means stat padders on bad teams get lower win shares than a guy who posts slightly less numbers but is on an elite team.
Meanwhile, win shares per 48 minutes is a measure of how good a player is "per-minute". For example, Karl Malone has a very high win shares number because he didn't miss a lot of games and had a very long career; however Tim Duncan trumps him in win shares per 48 minutes.

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