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49ers have a lot to consider when it comes to Colin Kaepernick

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Is Kaepernick's time with the 49ers over? (2:09)

Adam Schefter explains what Colin Kaepernick's benching means for his future with the 49ers. (2:09)

SANTA CLARA, Calif. -- San Francisco 49ers coach Chip Kelly doesn't know how many quarterbacks he plans to keep on his initial 53-man roster, but it's safe to say there will be at least two.

It's certain presumptive starter Blaine Gabbert will be one of them. But when it comes to what happens beyond Gabbert on the depth chart and roster, there's much more for Kelly and the Niners to consider.

When Kelly was asked Tuesday if Colin Kaepernick is one of the two best quarterbacks on the roster right now, he answered "yes." Under normal circumstances, that would leave no doubt that Gabbert and Kaepernick will occupy two roster spots. These days, things aren't quite so simple.

While Kaepernick has garnered attention and opinions from all corners of the country for his decision to sit during the national anthem, the 49ers still have to make a legitimate football decision when it comes to his status. It's a decision that comes with plenty of layers.

From a football standpoint, Kaepernick hasn't done much to stand out since Kelly arrived in January. Coming off knee, shoulder and thumb surgeries, Kaepernick missed most of the offseason program. Then, Kaepernick missed two preseason games and three valuable practices with the Houston Texans and Denver Broncos because of tightness in his right shoulder.

The lack of activity has left Kaepernick with a small sample size from which to judge, and the fact that he has played only 13 snaps in the exhibition season has left Kelly no choice but to play him in the finale against San Diego on Thursday.

"We're up against it," Kelly said. "And the fact that he missed those two games, it's unfortunate. But, we also have to look to the long-term future of the team, so there'll be some guys -- and again -- we haven't finalized any of that, so I won't be able to give you all of this and that of who's going to go, but it's not going to be the same line that he played behind when we played Green Bay."

Which means Kaepernick, who according to Kelly is still competing with Gabbert for the starting job, would have to come up with something pretty special against what will likely be Chargers backups to have a chance to unseat Gabbert.

To hear Kelly tell it, the 49ers haven't had any discussions about the quarterback group because the plan all along was to carry four on the roster through the preseason.

"I know everybody wants to know where this is going," Kelly said. "We haven't had one discussion about the quarterbacks because we had planned on having all four quarterbacks for the Chargers game. So our sole discussion was the cut to 75, and that's kind of where we are."

Perhaps the Niners haven't had the quarterback conversation yet, but it'd be foolish to think they haven't talked about them in some capacity. When they do get to the point where a decision has to be made, it might not be as simple as a football-only decision.

On Tuesday, Kelly indicated he and the coaching staff would like to make a decision on the starter after Thursday's game and an announcement could come as soon as Friday. The team will then have to go about cutting from 75 to 53. Kelly and offensive coordinator Curtis Modkins say they anticipate Kaepernick surviving that cut, but they also acknowledged it's not entirely up to them.

"I think it's a group thing," Kelly said. "There's always input. The final say is [general manager] Trent's [Baalke] and that's the way it should be. But it's not like I can say, 'Hey, I like these eight guys,' and he's like, 'I don't care about those eight guys. We're going this way.' We've got a really cooperative relationship as we're handling the team and moving forward, and I think the one thing about it is we see things the same way in terms of how to build a football team."

Kaepernick's relationship with Baalke has also received plenty of scrutiny. After the Niners attempted to trade Kaepernick in the offseason, he and Baalke didn't speak until early in training camp. Baalke called that a "good conversation." Asked a few days later if he would characterize it the same way, Kaepernick said, "We had a conversation." Kaepernick went on to say he and Baalke have a "business relationship."

The argument for keeping Kaepernick is he's clearly the most accomplished quarterback on the roster and would certainly have the best résumé of anyone behind Gabbert. If the Niners didn't keep him, the other options are sixth-round rookie Jeff Driskel and Christian Ponder, who was painting his house just a couple of weeks ago.

On the other side, there are some financial ramifications to consider. Kaepernick is set to make $11.9 million in base salary this year and has a $14.5 million salary next season that is guaranteed only for injury. In other words, if Kaepernick were to play this season and suffer a long-term injury that would keep him from passing a physical in the offseason, that $14.5 million salary would become guaranteed.

The Niners are already on the hook for Kaepernick's base salary this season but could potentially save some if he signed elsewhere because of offset language. And the Niners could easily handle the cap hit as they currently have the most salary cap space of any team in the league.

On top of all that, the Niners now have to deal with the possibility that if they don't keep Kaepernick, some will correlate the decision to his political stance no matter how many times they say it will be a football-driven choice.

"My dealings with Colin since April is when he's here, he's all about ball, and he's been great with that," Kelly said. "So that's what I deal with, and that's how we interact and he's been great. You guys watch him. When he's not in, he's mirroring the quarterback. He's getting as many mental reps as he can. He obviously had a setback in camp because of the shoulder, but from a football standpoint, he's been excellent."