Chip Kelly: Colin Kaepernick wants to play for 49ers

Editor’s note: Matt Maiocco is in Indianapolis to cover the NFL Combine. Check back for his comprehensive coverage and catch his nightly updates on SportsNet Central.

INDIANAPOLIS – New 49ers coach Chip Kelly has not gotten any indication from Colin Kaepeernick that he wants to resume his NFL career elsewhere.

Kelly said every time he has spoken with Kaepernick, there has never been a hint of discontent or any suggestion that he needs a fresh start.

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“He wants to be here,” said Kelly, who met with 49ers beat reporters for an hour Thursday at the NFL Scouting Combine. “He’s never expressed to me that he doesn’t want to be here. He expressed to me that he was excited about getting healthy and getting going. And we’re excited about him getting healthy and getting going.”

[MAIOCCO: Baalke: Kap will remain on 49ers in April, 'can't predict tomorrow']

Kaepernick is rehabbing from shoulder, knee and thumb surgeries in Vail, Colorado. Kelly echoed the words of 49ers general manager Trent Baalke, who guaranteed a day earlier that Kaepernick would remain on the 49ers’ roster during the offseason.

There was a lot of speculation the 49ers could work to part ways with Kaepernick, who was benched after eight games last season. Kaepernick’s scheduled $11.9 million base salary becomes fully guaranteed on April 1. Kaepernick and Blaine Gabbert are expected to compete for the 49ers' starting job.

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“I don’t know what the narrative is that, ‘Is he on the team? Is he not on the team?’” Kelly said. “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.”

Gabbert replaced Kaepernick as the 49ers' starter for the final eight games of the season after Kaepernick completed 59 percent of his passes with six touchdowns and five interceptions through the first half of the season. It's been quite a fall for Kaepernick, who lit up the NFL as a dual-threat quarterback in 2012.

“Kap’s really good,” Kelly said. “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.”

Kaepernick’s production has dropped incrementally since the 2012 season when he took over for Alex Smith and was the quarterback of the 49ers’ Super Bowl team. Kelly blamed Kaepernick’s dip in performance on the coaching change and injuries. Jim Tomsula replaced Jim Harbaugh last year, and the 49ers' offense struggled mightily under offensive coordinator Geep Chryst.

“I know he’s injured,” Kelly said. “People forget about that. He had a shoulder, a thumb and a knee that are legitimate. He’s the only guy I know who went on IR and everybody forgot he was injured. There’s a reason he was on IR.”

That’s why Kelly said Kaepernick’s first priority has to be completing his rehab and being 100 percent as the competition begins for the starting job.

“Getting a healthy Kap is an important thing,” he said. “And I’ve talked to him. He seems excited about where he’s heading and how that’s coming.”

Due to restrictions in the NFL’s collective bargaining agreement, Kelly is prohibited from speaking to Kaepernick about football until the beginning of the offseason program on April 4.

And because he can’t talk football with his players, he said it influences how he watches film, too. After all, Kelly said he evaluates only the skill of the players because he does not know the individual assignments.

That is something he keeps in mind while watching Gabbert, who oftentimes made the safe check-down throw on third downs that came up short of the yard markers.

“When I’m watching our film right now, I’m just analyzing skill sets,” Kelly said. “Like when I look at Blaine throw a check down, I don’t know what he was told to do and I don’t know what the play call was, so it’s hard for me to say, ‘Look at him, he’s wrong to make this decision.’ ”

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