SANTA CLARA, Calif. -- Those paying close attention know that San Francisco 49ers quarterback Colin Kaepernick, though a gifted runner, has produced at a high level from inside the pocket. They know quarterbacks can have it both ways.

Those paying close attention know the difference between a quarterback with running ability and a running quarterback. Kaepernick has been thrown into the latter category frequently enough for the characterization to fuel him. He thrives on defying misconceptions and has become quite perceptive to them.

Six months after leading the 49ers to the Super Bowl and failing to win it, Kaepernick senses a new criticism forming -- another myth to bust, in his eyes.

"In my mind, it's going to be, 'He can't win the big game,' " Kaepernick said from 49ers training camp recently. "To me, that is what I hear now."

It hurts being the first and only 49ers quarterback to lose a Super Bowl or to throw an interception during one.

"It happened," Kaepernick said, "but I'll be back. I'm going to win one. That is my goal right now, to go out and prove that, yes, that happened, but that is not who I am. That was a one-time deal."

Setting expectations

Early returns suggest that Kaepernick has a decent shot at becoming the first NFL player to reach 4,000 yards passing and 1,000 yards rushing in the same season.

Kaepernick's stats through 10 NFL starts, including three playoff games, project to more than 3,800 yards passing and 800 yards rushing over a 16-game season. Not bad for the sixth quarterback selected in the 2011 NFL draft.

2012 49ers QB Stats: Prorated for 16 Starts

The chart shows prorated 16-game totals for Kaepernick and fellow 2012 49ers starter Alex Smith based on their stats from the games they started. Their totals for passing touchdowns and interceptions are nearly identical, while the totals for passing yards and yards per pass attempt favor Kaepernick by fairly significant margins. However, the rushing stats are what truly separate Kaepernick, but should they define him?

"My biggest thing is, there is a huge difference to me between a running quarterback and a quarterback that can run," Kaepernick said. "And I think a lot of people just assume, 'Oh, he can run so he's a running quarterback. He must not mentally be able to take the game, and so he runs.' And I think that is what the perception is."

That perception feeds into the idea that Kaepernick is a one-read quarterback unskilled in working through a passing progression. Kaepernick said he's heard that one going back to his college days at Nevada. He points to specific plays with the 49ers when he bounced in his mind from one receiver to the next.

For example, Michael Crabtree was his fourth read on a 10-yard scoring pass delivered against Chicago in Kaepernick's first NFL start. That type of play won't compete with 50-yard runs for inclusion on a Kaepernick highlight package, but the skills he demonstrated were arguably more important for his long-term success.

A Kaepernick highlight package also won't include a presnap read Kaepernick made in that Chicago game. Kaepernick changed a play to exploit a certain defensive look, leading to a successful halfback run. He said that was the play from the Chicago game that offensive coordinator Greg Roman liked best.

"I don’t think there is any quarterback that is successful in the NFL that is one-read," Kaepernick said. "If you are sticking to one read, it’s going to be hit or miss, and your chances of hitting more than you miss aren’t very good. You have to be able to go through your reads to know what a defense is doing and where you want to go with the ball. To say you’re a one-read quarterback, those are the quarterbacks in my mind that don’t make it. They don’t play well."

Kaepernick trailed only Peyton Manning and Tom Brady in Total QBR last season for all plays and when rushing plays were excluded. That suggests he wasn't overly reliant on taking off with the football. Of course, the threat of running can create passing opportunities for a quarterback. That is presumably the case for Kaepernick.

QB as leader

Kaepernick generated considerable buzz this offseason by posing nude in ESPN The Magazine and for defying those who criticize controversial fashion statements. He wore sunglasses to the ESPYs and has reveled in a sneaker collection that would be the envy of any high school or college kid.

"You sit there and look at somebody on TV and say, 'This is all he does,' " defensive lineman Ray McDonald said. "But no, it's not like that. That is very ignorant of somebody to think that."

Three primary areas define Kaepernick's leadership in the team's eyes. He works hard, often arriving before 6 in the morning, and sets a standard in the weight room. He produces on the field, essential for any leader. And he interacts comfortably with coaches and teammates from all corners of the locker room.

McDonald, 28, has been with the 49ers since 2007. He has run hills with Kaepernick in nearby San Jose and has seen him pulling heavy chains around the practice field the way linemen typically would. He's played with a long list of lesser quarterbacks in San Francisco and knows a good one when he sees one.

"[Quarterbacks] control what is going to happen to us every single play, so you want that guy to be the leader of your team," McDonald said. "You want that guy to have that great work ethic, because it trickles down to everybody else, to the running backs, to the wide receivers, the O-line, the defense. When your quarterback is hot and he's working hard and doing what he has to do, we notice that as a team and that lifts everybody up.

"You see why Tom Brady has so much success and Peyton Manning and all those guys. It's just like that. They bring their team up with them."