Bill Belichick, and the Quarterback of the team, Tom Brady, are denying involvement and trying to minimise the issue. All this is doing is hurting the team, and hurting their reputations. Every quarterback in the NFL carefully adjusts the characteristics of the game balls - this has been done for a long time. It would seem like the NFL will give some kind of penalty to the Patriots. The Patriots low fumble rate appears to be statistically almost impossible - here is one analysis.
What we are wondering is that the Patriots might now have a big disadvantage in the Super Bowl. A team that is consistently used to under-inflated balls, might be at a disadvantage in the super bowl with balls that are correctly inflated; they won't be used to it. And it might also be a distraction for them. So this is all to the Seahawks advantage.
CNN did a good summary of Deflategate, SNL did a skit about Deflategate: