Today, the National Football League released Ted Wells' report on DeflateGate. It is damning towards Tom Brady and two attendants, but not to the New England Patriots organization as a whole. You can read the report in its entirety here.
The short end of it is that Tom Brady knew that the team was deflating balls and may have played a direct role in it. He also refused to hand over his text messages and e-mails to cooperate with the investigation. There is more substantial evidence that the two locker room attendants actually did in fact deflate the balls. I would suggest you check out page 75, where they discuss the New York Jets and how Brady was upset about the inflation of the balls in that game.
The more interesting thing to me is that despite the Patriots promise of full cooperation, there's evidence to show that they did not, in fact, fully cooperate with the investigation. As Wells states, "We believe the failure by the Patriots and its counsel to produce McNally for the requested follow-up interview violated the club's obligations to cooperate with the investigation under the Policy on Integrity of the Game & Enforcement of League Rules and was inconsistent with public statements made by the Patriots pledging full cooperation with the investigation."
However, there is little if no evidence that Bill Belichick knew about the air pressure of the balls. Despite that, as Roger Goodell once stated, "Ignorance is no excuse." Next, the NFL will decide the punishment for the Patriots. That will surely be entertaining to see.
EDIT: I'm seeing a lot of widespread confusion about the language of "more probable than not." Unless Wells caught Brady in the act of deflating the balls, he isn't going to say it's conclusive, from a legal perspective, even though the evidence he uses to demonstrate his point shows it's pretty conclusive. This isn't a criminal trial where he needs to prove "beyond a reasonable doubt."