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Colin Kaepernick over Alex Smith: Jim Harbaugh elevates 49ers

What is Jim Harbaugh doing in San Francisco?

That's a question some folks are asking after the San Francisco 49ers head coach named Colin Kaepernick the starter, despite the healthy return of Alex Smith. In making the decision, Harbaugh opts for a second-year player with two career starts over an eight-year pro with a 19-5-1 record since Harbaugh's arrival in 2011.

While some have suggested this bold decision will undermine San Francisco's Super Bowl chances due to Kaepernick's inexperience, I believe the move to the more athletic playmaker will reap huge benefits for the 49ers in the short and long term. After studying the All-22 Coaches Film, here are three reasons why:

1. Kaepernick allows the 49ers to incorporate more quarterback runs.

Prior to being drafted 36th overall in the 2011 NFL Draft, Kaepernick was an outstanding dual-threat quarterback at the University of Nevada (Reno). He is the only player in NCAA history to pass for 10,000 yards and rush for 4,000 in a career. In addition, he was the first major college player to throw for 2,000 yards and rush for 1,000 in three straight seasons. Those ridiculous numbers not only speak to his explosiveness as a runner/passer, but they support Harbaugh's desire to put a more dynamic playmaker on the field at quarterback.

With an explosive athlete taking the snap from center, the 49ers create problems for defensive coordinators with the threat of the quarterback run. In theory, defenses don't account for the quarterback in the running game, utilizing the extra defender as a free hitter in the box. (Defenses employ eight-man fronts on early downs against two-back sets because it gives them a numerical advantage at the point of attack when the quarterback isn't used as a runner or blocker.) Kaepernick's presence eliminates that advantage and provides San Francisco with a variety of ways to exploit defensive tactics.


San Francisco's reliance on the power run game out of two-back sets makes the bootleg an effective counter to overaggressive defenses. When the 49ers sense the opponent pursuing hard to running back Frank Gore, they can elect to run a few bootlegs to the backside to take advantage of undisciplined defenders.

In the following screengrab from the 49ers' 34-0 win over the New York Jets in Week 4, San Francisco breaks the huddle in an I-formation with the tight end to the left. The Jets, anticipating a Gore run, have nine defenders in the box:

Kaepernick fakes the ball to Gore on an isolation play, which draws all three Jets linebackers to the line of scrimmage:

After the fake, Kaepernick keeps the ball and takes off around the right end:

The result? Kaepernick ran 30 yards untouched before sliding inside the 5-yard line (a classy move with the Niners leading 34-0 and under two minutes remaining in the game).


Like I discussed above, the quarterback is unaccounted for in most NFL defensive schemes, creating big-play opportunities for the 49ers on predetermined quarterback runs. Harbaugh has exploited this tactic in the past with Smith (most notably in last year's playoff win over the New Orleans Saints), but he will take it to another level with Kaepernick at the helm. Even before he took over the starting job, Kaepernick ran plenty of straight sweeps for the Niners this season.

In the screengrab below from the Jets game, the 49ers align in a shotgun formation with a trips bunch alignment to the left. Kaepernick will run the quarterback sweep with the three receivers executing crack-back blocks on their assigned defenders on the perimeter:

Kaepernick takes the snap and runs around the left end with Gore and left tackle Joe Staley leading the way:

This produces a seven-yard touchdown.


Kaepernick masterfully directed the Pistol formation at Nevada, with the zone-read as the primary play. The 49ers have incorporated a Pistol package into their larger game plan with outstanding success. For the defense, the option poses a challenge because it forces each defender to play with assignment discipline. If one defender fails to attack his designated hole or run to his assigned player, the 49ers can exploit the miscue for a big gain on the perimeter.

In the next screengrab from the 49ers' 45-3 win over the Buffalo Bills in Week 5, the team breaks the huddle in the Pistol with an inverted wishbone alignment by the running backs:

On the snap, Kaepernick sticks the ball into Kendall Hunter's belly and reads the reaction of Bills DE Mark Anderson:

After Anderson crashes down to stop Hunter, Kaepernick pulls the ball back and heads for the edge:

Sixteen yards later, another San Francisco touchdown.

The additional benefit of utilizing the zone-read is the effectiveness of the package near the goal line. Most defensive coordinators utilize man-to-man inside the 10-yard line, which keeps defensive backs from getting involved in run stopping due to their assignments in coverage. With the zone-read frequently putting the quarterback on the perimeter following a fake, the 49ers are able to generate explosive plays on the ground using misdirection and deception.

In the following screengrab from the 49ers' tie with the St. Louis Rams in Week 10 -- the game in which Alex Smith was concussed -- the team breaks the huddle in the Pistol, with an offset I-formation following motion from Delanie Walker:

Kaepernick takes the snap and immediately puts the ball into Gore's belly as he reads the reaction of Rams DE Chris Long:

Once Long commits to attacking Gore, Kaepernick keeps the ball and turns the corner with blockers downfield:

The 49ers' receivers lock up the Rams' defensive backs on the second level, allowing Kaepernick to scoot in for a seven-yard touchdown.

With Kaepernick's running skills adding another dimension to the 49ers' powerful ground game, defensive coordinators around the league will find it more difficult to stop San Francisco down the stretch.

2. Kaepernick's superior arm strength provides a vertical dimension.

Kaepernick was regarded as one of the most impressive talents in the 2011 draft class due to his exceptional arm strength. He displayed the capacity to make every throw with zip and velocity. In addition, he showed outstanding deep-ball touch and accuracy.

Watching the 49ers' offense in the past, I noticed that the lack of a vertical passing game allowed opponents to creep up to the line of scrimmage to clog running lanes and disrupt the timing of the quick-rhythm passing game. With Kaepernick at the helm, the 49ers will push the ball down the field and take advantage of some of the one-on-one matchups on the outside. This will allow the 49ers to take full advantage of the collective talents of Randy Moss, Mario Manningham, Vernon Davis and Walker.

In looking at the 49ers' last two games, it is apparent that Harbaugh is capitalizing on the vertical passing game with Kaepernick under center. Kaepernick has registered 11 completions of 20-plus yards and three passes of at least 40 yards. Those numbers are certainly eye-popping when compared to Smith's 22 20-plus yard completions on the season. With big plays valued at a premium, particularly in the playoffs, the decision to go with the bigger arm could pay huge dividends for the 49ers down the stretch.

3. The 49ers will see fewer blitzes due to Kaepernick's athleticism.

The insertion of Kaepernick into the lineup changes the way opponents defend San Francisco. Instead of bringing heavy pressure with man coverage in the back end, opponents will scale back on five- and six-man blitzes for fear of surrendering big plays on impromptu scrambles. In man-to-man, defensive backs are locked onto their assigned receivers with their backs to the action. This prevents them from reacting quickly when Kaepernick flees the pocket, leading to big chunks of yards on scrambles.

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In studying the All-22 footage from the 49ers' past two games, I'm impressed with Kaepernick's ability to elude defenders in the pocket. He selectively scrambles when he sees creases in the middle of the field. These improvisational runs have routinely led to first downs, sustaining drives and frustrating defensive coordinators looking to make the perfect call.

In the screengrab below from the 49ers' 31-21 win over the Saints last week, Kaepernick sees seven defenders within five yards of the line of scrimmage on third-and-6, indicating a likely blitz:

After the snap, the Saints bring six defenders, with an overload blitz to Kaepernick's right:

When Kaepernick isn't able to find his primary receiver down the field, he spots an open lane in the middle and takes off:

This play resulted in a 15-yard gain and a fresh set of downs.

Follow Bucky Brooks on Twitter @BuckyBrooks.

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