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Chip Kelly: Never been a question about having Kaepernick on team

at Levi's Stadium on November 8, 2015 in Santa Clara, California.

at Levi’s Stadium on November 8, 2015 in Santa Clara, California.

Ezra Shaw

There was a lot of discussion heading into the offseason about what the 49ers would do with quarterback Colin Kaepernick, who is due to have his salary for next season guaranteed on April 1 after a season that saw him struggle on the field before heading to injured reserve and having three surgeries.

There were also reports that Kaepernick didn’t want to remain with the 49ers, but General Manager Trent Baalke let the air out of the balloon on one front Wednesday. Baalke said that Kaepernick will be on the roster beyond April 1 and that he will compete with Blaine Gabbert to be the team’s starting quarterback.

On Thursday, coach Chip Kelly said that Kaepernick “wants to be here” and that he never wanted to come to the 49ers in order to get rid of the quarterback.

“I don’t know what the narrative is that, ‘Is he on the team? Is he not on the team?’” Kelly said, via “It’s never been a question. I’m excited to work with Colin. I’ve never thought that, ‘Hey, I’m going to go to San Francisco and he’s not going to be there.’ I don’t know why everybody else looks at it that way, either. ... Kap’s really good. He had the ball on the 5 yard line, taking the team in to win the Super Bowl. You can just look at the tape and know how talented he is. Our job is acquiring talent, not getting rid of talent.”

Kelly said the important thing for Kaepernick in the short term is to get healthy so that he can put forth his best effort in both getting the offense down and competing with Gabbert. At his best Kaepernick has looked like a good fit for what Kelly wants from his quarterbacks, which should make that competition one of the more interesting ones to watch play out in the spring and summer.