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The San Francisco 49ers finished the 2012 season with the 11th-highest scoring offense in the NFL, averaging a full 66 yards fewer per game than the New England Patriots, who finished in first place. Despite that ranking, a legitimate argument could be made that the 49ers had the best offense in the league once Colin Kaepernick became the starting quarterback.

With Kaepernick, the offense averaged 28.8 points per game in the regular season and the playoffs. In the games that Alex Smith started (and finished), the 49ers averaged 23.6 points per game.

Kaepernick's impact was so great that he was almost immediately pushed into that class of superstar youngsters from the 2012 rookie class. In fact, not only was Kaepernick put on the same level as Andrew Luck, Russell Wilson and Robert Griffin III, one analyst even singled him out as a player with the potential to finish amongst the greatest players ever to play his position.

It was ESPN's Ron Jaworski who stated, "I truly believe Colin Kaepernick could be one of the greatest quarterbacks ever. I love his skill set. I think the sky's the limit."

From a sheer physical perspective, there is no arguing with Jaworski's statement.

Kaepernick has that rare type of athleticism that allows him to do almost anything. He can probably outrun any player in the league in a straight sprint, but he also has the acceleration and balance so that every bit of his straight-line speed translates onto the football field.

As a passer, he can flick the ball further than some quarterbacks do with a heave, while the velocity of his passes is on that elusive Cam Newton and Aaron Rodgers level.

Once that physical talent was inserted into an offense with probably the best offensive line in the league, an overwhelmingly talented group of running backs, arguably the best receiving tight end in the NFL, an emerging young star at the wide receiver position and probably the best offensive coaching staff in the NFL, it was no surprise that the unit flourished.

It's easy to judge an offense by how many points it produces. It's not always an accurate judgment, however.

The 49ers' goal on offense isn't to score 40-plus points per game. That's not the way they have set up their team. Instead, the 49ers use their offense to control the game by methodically moving the ball down the field. This allows them to minimize turnovers and control the clock, while still putting a lot of points on the board when they need to.

In the modern NFL, teams are desperate to build complex and incisive passing attacks. The 49ers haven't gone in that direction. As lauded as Kaepernick is for his arm talent, the 49ers offense is very much committed to building the attack on the strength of their running game.

The most celebrated aspect of that running game is undoubtedly the team's read-option package.

Read-Option

Although it's a massive talking point for most sections of the media, the 49ers didn't use read-option plays that often last season. From the time Kaepernick took over as a starter against the Chicago Bears, he played 640 total snaps (via Pro Football Focus). Of those 640 snaps, 69 were definitely read-option plays.

While it wasn't used that often, the read-option was very effective for the 49ers. More often than not, teams forced the play inside to the running back, but even when they did that, Kaepernick's outside threat helped the offense average over five yards per carry.

More damage was caused when defenses allowed the quarterback to take the ball. Kaepernick had four runs of at least 10 yards from option plays, with two of those four going for at least 50 yards. In comparison, the 49ers backs had less than double that number on nearly four times as many attempts.

On one play against the St. Louis Rams, the 49ers ran a triple option with Ted Ginn, a wide receiver, running behind the line of scrimmage. On that play, Kaepernick missed the pitch to Ginn, resulting in a 12-yard loss and a touchdown for the Rams.

That was the only play of the season when the 49ers involved a wide receiver on an option play. At least it was the only time when a wide receiver was used as a running option.

The above chart makes it clear that forcing the ball into the running back's hands is the best option against the 49ers. However, like any analytical chart, the defense has a major impact on those results.

On this chart, the previous numbers are broken down on an opponent-by-opponent basis.

It's clear that the New England Patriots and Seattle Seahawks defended the read-option better than any other team.

The Saints gave up fewer yards per attempt, but they also allowed the 49ers to score a touchdown in the first quarter. On that play, Saints defensive end Will Smith didn't commit to Kaepernick or the running back, allowing Kaepernick to escape outside for an untouched seven-yard score. The Rams scored that touchdown against the 49ers, but they didn't face another option play in the whole game.

Against the Patriots and Seahawks, Kaepernick was forced to hand the ball off to the running back on every single read-option play. The Patriots faced 10 read-option plays, holding the 49ers to gains of three or fewer yards on five of them.

Discipline, aggression and an abundance of talent is required to contain the option offense.

Every member of the front seven must be very disciplined to maintain the integrity of the defense. The edge defender to the option side of the play must be in a position to force the ball to the running back, but also in a position that allows him to prevent any cutback from the back.

The linebackers inside must be decisive at the snap to immediately attack the line of scrimmage, while the interior defensive linemen can't get trapped upfield.

On the above plays, the Patriots show off discipline, aggression and the talent on the defensive line not to be pushed off the line of scrimmage. The 49ers gained a total of two yards on these plays.

When the 49ers had their longest run of the game, it was the Patriots' linebackers who let the defense down.

The 49ers came out in a formation that took them away from any read-option plays. Kaepernick was under center, with Gore behind him and a tight end to either side of the formation. Because Kaepernick has to turn from underneath center and go back to Gore, he can't make any read on the defense before he hands the ball off.

Therefore, he can't run the read-option.

It's 1st-and-10, yet the Patriots have come out in a 4-3 formation with their two defensive ends standing up. Chandler Jones is lined up over Vernon Davis in the slot, with Rob Ninkovich lined up over Bruce Miller on the other side. Because the linebackers are expecting to have more time to react to any run plays, they have lined up in deeper positions at the snap.

As they often do, the 49ers shift their offense into a new formation before the snap. Kaepernick drops back to create a pistol look, with Miller and Davis also dropping into the backfield. The Patriots react by motioning one of their linebackers to the edge of the offensive line and by pushing Jones infield so he is lined up across from the 49ers' left guard.

The Patriots now have five defensive players at the line of scrimmage, but their other two linebackers still have the same level of depth they initially lined up with. Because the 49ers essentially have seven blockers (five offensive linemen and the two players in the backfield alongside Kaepernick), the Patriots are outnumbered at the line of scrimmage still.

As the read defender, Ninkovich plays his assignment as well as he could have. He doesn't rush down the field or come inside too much, meaning that he forces the ball into the running back's hands while still being in a position to stop any cutback.

While Ninkovich's hesitation actually benefits the defense and is there by defensive design, the hesitation of the two inside linebackers is unwanted. That hesitation allows Alex Boone and Anthony Davis to double-team defensive tackle Kyle Love, highlighted by the red circle.

Love is pushed back into the two waiting linebackers, allowing Gore an easy read to completely take one of them out of the play. The end result is an easy eight-yard gain.

Had either linebacker been closer to the line of scrimmage, Love wouldn't have faced a double-team and the Patriots could have created a wall to force Gore back towards their free linebacker.

Therefore, it's not only important for the edge defender to be disciplined and aggressive; defending the read-option needs all pieces of the front seven needs to share that approach.

This is why pushing the ball infield to the running back on option plays is always better than allowing the quarterback to get outside. If the outside defender is less disciplined, the quarterback is released into space against cornerbacks. If an inside defender has a misstep, then there is still a tighter area to run through. Instead of cornerbacks, safeties and linebackers are more likely to be making tackles.

It's true that the read-option is only a part of the 49ers' rushing arsenal, but the hesitation it causes in defenders is something that the offense as a whole looks to create.

A Creative, Diverse Rushing Attack

Andy Benoit of the MMQB recently wrote, "The Niners might be the only offense left that lines up and implicitly says, 'Here's our run game; try to stop it.'"

Benoit is completely right in his statement for many, many reasons, but don't be fooled into thinking that he is saying the 49ers' running game is a simplistic thing.

It's easy to say that running offenses just line up and run over people today. The NFL celebrates creative and diverse passing offenses for the most part, whereas running the ball is a necessity that just reminds us of old-school, unimaginative football.

Nobody would ever say that the New England Patriots or Green Bay Packers are simply throwing the ball past people. Yet many will say the 49ers or Houston Texans just run over people. That is oversimplification.

Within the 49ers' running game, you have many diverse pieces managed by a very creative coaching staff. Kaepernick is a cheetah posing as a human being. Frank Gore is a miniature rhino with a brain twice the size of a sperm whale. If Kaepernick is a cheetah, LaMichael James is his cub. Kendall Hunter offers the same variety as Gore, just to a lesser degree.

Most will know Kaepernick and the backs in San Francisco. Most will know how good they are.

However, just like any other rushing attack in the league (outside of Adrian Peterson), the key to stopping them is winning at the line of scrimmage.

Of course, the only problem with that is it's like saying the only thing you need to do to stop the Detroit Lions offense is stop Calvin Johnson.

The 49ers have the best offensive line in the NFL. Three first-round picks, a converted tackle who has flourished at guard and a Super Bowl-winning center were brought together to create the unit.

Left tackle Joe Staley is the leader of the unit. Today's league is full of left tackles who can consistently shut down pass-rushes from snap to snap. However, most of those left tackles are ineffective or even a liability as run-blockers because of the way they are built.

Staley isn't like that.

Staley can shut down the very best pass-rushers in the league, but he is also an outstanding run-blocker. Some left tackles in the NFL can maul defensive ends or tight ends to the ground or push them back into the secondary. Staley can do that better than anyone, and he can also seal off defensive tackles inside, pull into space or advance to the second level to block linebackers.

That combination of traits makes Staley a unique player in today's league. Unless Jason Peters returns to his dominant form of 2011, there won't be another left tackle in the league who does as much for his team in 2013.

With a player like Staley, most teams would look to build their rushing attack off of him. The 49ers don't—because they don't need to.

There are specific plays that take advantage of his different abilities, but with Alex Boone and Mike Iupati at the guard positions and Anthony Davis at right tackle, the 49ers can attack any area of the defense at any given moment in different ways.

Boone is a former offensive tackle who had a skill set that perfectly translated to guard in the 49ers scheme. Iupati was a high first-round pick who has all the talent to be the best guard in the league. Davis was also a first-round pick who has cemented his place as one of the best right tackles in the NFL.

Davis is a mauler who uses his bulk to overwhelm defenders, but Iupati and Boone make the offense special. Just like Staley, Iupati and Boone can do a variety of things and do those things at an extremely high level. As a defensive lineman lining up across from either guard, you never know where they are going or how they will get there.

Most guards can do a few things, such as sliding to one side or hitting defenders at different angles. The 49ers guards can do all of those things, but they also pull to the outside or across the formation, trap defensive tackles after pulling from different positions, move to the second level to locate a linebacker or drop out as screen protectors.

A majority of defensive linemen are overwhelmed by the sheer physical talent of the 49ers' offensive line. Those who aren't are still put at a disadvantage because most can't cope with the diversity of the rushing attack. Creating hesitation is what the 49ers thrive on, and it's what can cripple defensive linemen.

They can create gaps as individual blockers who stay in position:

They can slide to one side to trap defenders in the backfield as the back escapes outside:

They can clamp down both sides of the line while bringing a guard from either side across the formation:

They can slide the line to one side while pulling the guard outside the tackle in the same direction:

They can send more than one blocker into the secondary immediately at the snap:

Defending the 49ers' running game is similar to wrestling a bear while wearing stilts on roller skates and running through a pothole-filled road. You're probably overpowered, you're off-balance and even if you solve both of those things, you can still fall in a pothole as you try to take down the back.

Besides the plays that are primarily reliant on the offensive line's ability, the 49ers use a lot of misdirection to further throw defenders off-balance.

On this play, Frank Gore lines up next to Kaepernick in the backfield with LaMichael James in the slot to the bottom of the screen. At the snap, James turns and runs back towards Kaepernick, who turns his back to the defense to hand the ball off to him on the end-around.

When Kaepernick turns to face James, the Ravens are expecting him to either give the ball to James or turn and run with him towards the opposite sideline. Instead, Kaepernick slips the ball to Gore, who is moving towards the side where James initially lined up. With Gore, the 49ers are pulling Iupati from the left guard position and bringing Delanie Walker across with him.

That gives Gore a convoy to lead him to the sideline, while Ray Lewis in the middle of the field is still trying to figure out where the ball is.

If the 49ers running game was a passing attack, it would be like having A.J. Green and Julio Jones as your outside receivers with Wes Welker and Percy Harvin playing in both slots as Jimmy Graham works at tight end. There is just no way you can shut the unit down completely or match up to everything that they can throw at you.

Except it's not just like that. It's like having those pieces and putting them in a perfectly designed offense.

According to the Football Outsiders Almanac, 74 percent of their runs last season came with two backs on the field, the most in the league. A league-high 48 percent of their snaps used some combination of two backs or two tight ends, while they used two backs and two tight ends 24.2 percent of the time, much more than anyone else in the league.

Those raw numbers should reflect on a rigid offense that runs out of the same formations very often, an offense that pulls the defense in tight as opposed to spreading it across the field.

It's true that the 49ers do run a lot of tight formations, but their offense is far from rigid. The personnel that they had last season, Bruce Miller at fullback with Delanie Walker and Vernon Davis at tight end, allowed the 49ers to be very flexible with their formations.

That flexibility made them a very fluid and unpredictable offense.

Most of the 49ers' formations allow them to run the ball, but more often than not there is an element of misdirection or a play-action threat that comes with them. As the season wore on last year, they began to use more and more of the pistol formation because it offered that read-option, bootleg and simple play-action threat for the quarterback.

There isn't a way to shut down this offense, even without considering Kaepernick's influence in the passing game.

But there is a way to put the unit in uncomfortable positions and shift the focus away from the running game.

Stopping the Offense

Third-and-7 is a sweet spot for any defense. It means the offense is behind in the count in a sense, as they have greater gains to achieve on fewer downs.

The 49ers saw very few 3rd-and-7s with Kaepernick as their starting quarterback last season. When they did, they struggled to convert them.

The distance from the line of scrimmage isn't really the issue for the 49ers, at least not directly. The issue with 3rd-and-7 or more for the 49ers is that it takes the balance out of their offense. Even though they don't run the ball over 60 or 70 percent of the time, the 49ers are very much a run-reliant team that uses the threat of the run to set up the pass.

According to the Football Outsiders Almanac, the 49ers ran the ball 50 percent of the time on first down for the whole season last year. Often when they threw the ball on first down, they were making quick passes to already open receivers that were essentially elongated handoffs.

Their desperation to get yards on early downs is born out of the need to put Kaepernick in specific situations. Kaepernick is a very precise passer with exceptional arm strength. But like most young quarterbacks, he doesn't read through progressions well, can struggle with pressure in the pocket and often allows his eyes to drop from the secondary too early.

Much of Kaepernick's role in the 49ers offense is based around his ability to find his first read. Because teams are forced to play more zone against him to account for his running threat, and because his offensive line is able to offer him huge amounts of time in the pocket, Kaepernick can keep his eyes on one receiver for much longer than most quarterbacks.

On 3rd-and-7, the run threat disappears. Teams are more willing to play man coverage and can get a better pass rush.

On plays that aren't 3rd-and-7 or more yards, teams are unable to be creative with how they blitz Kaepernick. Creative blitzes or coverage shifts are often done to overload gaps in the offensive line. With a running threat at quarterback, teams can't overload one gap because they expose themselves to big gains on the ground.

When Kaepernick faced creative blitzes or coverage shifts at the snap, he struggled.

On this play, it's 3rd-and-8 and the Bears are threatening to blitz with each of their three linebackers pressed to the line of scrimmage. The 49ers set up their offense early, giving Kaepernick time to alter protections and direct his offensive line before the snap.

Kaepernick sets up his protection to give him enough time to make a quick decision with his two receivers to his left. Those two receivers are crossing each other with the slot receiver going to the sideline and the outside receiver coming infield. That should allow Kaepernick to get the ball out almost immediately and for the receiver to get a first down or touchdown with good YAC ability.

However, the Bears drop those three linebackers into coverage immediately at the snap.

The linebacker to the left side of the offense was actually a defensive back, Kelvin Hayden. Hayden immediately takes away Mario Manningham's route coming infield, where Kaepernick is looking. Kaepernick sees him at the last second to stop his throwing motion.

As he resets himself, he is hit from behind by Israel Idonije. Idonije beat right tackle Anthony Davis with ease and Davis didn't react at all when he went by him, so it appeared that he was expecting help from Gore. Gore was on the other side of the formation, however, as he expected to pick up a blitz coming from that side. A blitz that never came.

In order to stop the 49ers offense, you must put them into these positions. In order to do that, you must stop the run with a disciplined front seven that has talent on the interior of the defensive line, but you also must play very aggressive coverage in the secondary.

Aggressive, but also smart coverage.

Limitations of the Passing Game

Kaepernick's worst passing display last season came against the Seattle Seahawks. Critically, the Seahawks took away the running game from the 49ers by jumping out to an early lead and playing disciplined, aggressive defense with very talented pieces in the front seven.

Once that happened, the Seahawks were able to be more aggressive on the 49ers' underneath throws.

The Seahawks trusted their secondary to handle the 49ers receivers and dared them to throw the ball deep. As strong as Kaepernick's arm is, his deep accuracy is still very inconsistent. Most of his success on deep passes came when receivers or tight ends had run crossing routes or out routes and there was a greater window for him to throw into.

Rarely did the 49ers actively look to throw the ball down the sideline against man coverage, because those throws required accuracy that Kaepernick didn't consistently have.

Here is Kaepernick's passing chart from the Seahawks game:

The Seahawks dared the 49ers to consistently throw deep at their talented defensive backs. A handful of positive plays came, but nowhere near enough to sustain a winning offense.

At the beginning of this piece I pointed out that the 49ers don't have a wide-open offense that looks to score 40-plus points in every game. They have a methodical offense that looks to control the game and link plays together consistently.

The issue with that approach is that only one or two parts of the offense need to collapse for the series to be all but over.

In order to stop the 49ers, you must have a huge amount of discipline in the front seven with nearly as much talent. You must also be aggressive with your safety play and trust your cornerbacks to contain receivers going down the field.

Above is Kaepernick's passing chart for the 2012 season. It shows how the 49ers prefer to throw outside and underneath instead of pushing the ball down the field. The new receiving options in San Francisco this season fit that same kind of offense, despite how often Anquan Boldin went deep during last year's playoffs.

In spite of what Boldin, Quinton Patton, Austin Collie or Vance McDonald can bring to the offense, none will be able to replace the massive loss that comes with Michael Crabtree's torn Achilles tendon.

Crabtree is the smartest receiver in the NFL with the ball in his hands. He doesn't have the same explosion as a Percy Harvin or Tavon Austin, but he knows how to manipulate defenders and expose them in space.

Being a good runner after the catch isn't solely about acceleration, straight-line speed or quickness. Crabtree's two most valuable traits are his understanding of situations and his understanding of how to set himself (and the defender) up at the point of catching the football.

Often Crabtree will catch the ball in an unorthodox way that would be uncomfortable for most receivers. It looks like he is making the reception unnecessarily more difficult, but it's those subtle movements that allow him to glide away from defenders with ease.

After Kaepernick took over as the starting quarterback, he threw for 2,162 yards. Crabtree accounted for 880 of those yards, with 393 coming after the catch. Crucially, Crabtree caught 19 passes from Kaepernick that turned into either a touchdown or a first down primarily because of his ability with the ball in his hands.

Crabtree's consistency in how he manages situations, sets up defenders and uses his speed/strength to create big plays made Kaepernick's job much easier last season. Often the quarterback didn't have to make a pinpoint pass or throw the ball down the field in order to get a big play.

Without him in the lineup, the 49ers' threat on the outside figures to suffer a dramatic drop-off.

If Kyle Williams and Mario Manningham are fully healthy, they will offer a different kind of threat across from Anquan Boldin, but none of the other receivers on the 49ers' roster are anywhere near the level of the former Texas Tech prospect.

Without Crabtree, the 49ers will likely rely heavily on tight end Vernon Davis for their big plays. Davis is one of the best receiving threats in the NFL, but his usage in the running game along with the lack of options to pull coverage away from him should quell his impact somewhat.

Depending on how Kaepernick develops, the 49ers offense could be close to unstoppable even without Crabtree. However, that would require Anquan Boldin to play at the same level during the regular season this year that he played to during the postseason last year. Boldin elevated his game when the lights were brightest last year, but he was a shell of himself during the regular season.

If Boldin reverts back to his regular-season form, the 49ers will need Colin Kaepernick to elevate himself as a quarterback to the point that he can make his receivers better. As Ron Jaworski pointed out, Kaepernick has all the physical tools; he just needs to develop.

Development is often taken as a given, but there are many examples of players who never reached their true potential. It's still very early to crown Kaepernick.

The 49ers have arguably the best coaching staff in the NFL and an incredible level of talent to put on the field. You won't stop this offense with an average group of defensive players or even with a talented group of players who are poorly coached.

You need both, because the offense certainly has both.

You can follow Cian Fahey on Twitter @Cianaf