When head coach Kyle Shanahan and general manager John Lynch took over control of the 49ers in 2017, they told quarterback Colin Kaepernick that he would be released if he didn't elect to opt out of his contract. Kaepernick indeed chose to back out of his deal, and the signal-caller hasn't played a down in the NFL since.
Kaepernick was coming off a season in which he had completed 59 percent of his passes and thrown 16 touchdowns with four interceptions over 12 games. While general managers tend to want to bring in their own talent at key positions like QB, Pro Football Focus' version of the "Wins Above Replacement" statistic shows that Kaepernick was an extremely valuable player during his time in San Francisco.
— PFF (@PFF) June 5, 2020
As you can see from the 49ers' top five, the stat seems to favor quarterbacks. According to the website's in-depth breakdown of PFF WAR, the model does these things in analyzing statistics:
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Determine how good a given player was during a period of time (generally a season) using PFF grades;
Map a player's production to a "wins" value for his team using the relative importance of each facet of play;
Simulate a team's expected performance with a player of interest and with an average player participating identically in his place. Take the difference in expected wins (e.g., Wins Above Average);
Determine the average player with a given participation profile's wins above replacement player, assuming a team of replacement-level players is a 3-13 team;
Add the terms in the last two calculations to get that player's WAR.
The conversation around Kaepernick's absence from NFL rosters over the past three seasons has reignited in light of protests around the country following George Floyd's tragic death while in Minneapolis Police custody. Kaepernick sued the NFL claiming that the league blacklisted him because of his choice to kneel during the national anthem. The NFL settled out of court with Kaepernick in February of 2019.
Kaepernick did lead the 49ers to the Super Bowl in the 2012 season, breaking the NFL record for rushing yards by a quarterback in one game (181). In 69 career games with the 49ers, Kaepernick threw for 12,271 yards and 72 touchdowns.
Vernon Davis had 454 catches and 55 touchdowns as a Niner after being drafted in the first round of the 2006 NFL Draft. Davis was traded to the Denver Broncos for draft compensation during the 2015 season, but was a sensational pass-catcher during his time in the Bay Area. He also was on the receiving end of one of the franchise's most iconic moments of the 21st century.
The website's description also indicates that players who line up further away from the center of the line of scrimmage tend to score higher (i.e. wide receivers, defensive backs, tight ends) which is why Joe Staley's place on this list shows just how valuable the left tackle was during his 13-year tenure in San Francisco.
NFL commissioner Roger Goodell said in December that the league has "moved on" from Kaepernick, but this conversation doesn't seem to be going anywhere for the league's senior leadership.
Colin Kaepernick was 49ers' most valuable player of decade, per PFF originally appeared on NBC Sports Bay Area