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The San Francisco 49ers decided it wasn't worth waiting any longer to lock up their franchise quarterback for the long haul.

The Niners signed Colin Kaepernick to a six-year contract extension through the 2020 season that makes him one of the NFL's highest-paid players.

NFL Network reported the deal is worth up to $126 million with $61 million in guarantees, which would surpass Drew Brees' $60.5 million on the deal he signed in 2012 with the New Orleans Saints for the most guaranteed money in NFL history.

The structure of the deal will be telling. The 49ers were less than $1.6 million under the salary cap as of Wednesday afternoon, per NFL Players Association records, but that was before a post-June 1 designation for cornerback Carlos Rogers cleared another $6.6 million in cap space.

Kaepernick was due just $973,766 in base salary plus a $100,000 workout bonus in the last year of his rookie deal.

"Colin's hard work and dedication have played an integral role in the recent success of the 49ers organization," 49ers general manager Trent Baalke said in a statement. "His work ethic, leadership and on-field production have positively influenced our team, and we look forward to his continued growth in all areas.

"Our organization always looks to reward our players for their contributions and commitment to the team. Colin's agents, Scott Smith and Jason Bernstein, along with Paraag Marathe and Brian Hampton, should be commended for working diligently to reach an agreement."

Kaepernick, 26, has passed for 5,046 yards and 31 touchdowns with 11 interceptions over three NFL seasons and added 937 yards and nine scores as a runner. He took over for Alex Smith as the 49ers' starter midway through the 2012 season and has appeared in consecutive NFC Championship Games and Super Bowl XLVII.

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