Kaepernick takes stab at free-agent market

INDIANAPOLIS — For the first time in his career, Colin Kaepernick is not under contract with the 49ers.

That inevitability became official Friday when the quarterback filed paperwork to opt out of the final year of his contract. Kaepernick will hit the open market when free agency begins Thursday.

Head coach Kyle Shanahan and general manager John Lynch have acknowledged Kaepernick, 29, would opt out of his contract this week at the NFL combine.

Lynch indicated the 49ers would have released Kaepernick if he didn’t opt out. Kaepernick was scheduled to earn a $14.5 million base salary in 2017. His exit leaves the 49ers without a quarterback under contract for next season, although neither Lynch nor Shanahan have ruled out re-signing Kaepernick.

“I think we both agreed that under the current construct it wasn’t going to work out,” Lynch said. “But we said let’s not close the door, and we had some good jokes. Once he was gone, we weren’t going to have (a QB). As he hits free agency, that’s something that we’ll keep our eyes open and we want him to keep us in mind as well. So, it’s something that we left that door open in a very real and positive way.” Talking up trenches: Lynch acknowledged Thursday the 49ers “need players,” but it sounds as though they may not be shopping for many guards, centers or tackles this offseason.

Asked about an area of strength on a team that went 2-14 last season, Lynch cited the offensive line, which allowed the third-most sacks in the NFL (47).

“I think offensive lines are tough to build in this league,” Lynch said. “And you turn on the film and there’s a lot of exciting things to see with an offensive line.”

The 49ers did rank 10th in the league in yards per rushing attempt (4.4), and they could return the same unit in 2017. They have a pair of promising young starters in right tackle Trent Brown, 23, and right guard Joshua Garnett ,23,a 2016 first-round pick. The front five is rounded out by Pro Bowl left tackle Joe Staley, left guard Zane Beadles and center Daniel Kilgore, who has missed 23 games since 2014 due to injury.

Lynch said the 49ers had the potential to be tough in both the offensive and defensive trenches. He said the defensive line, which includes recent first-round picks Arik Armstead and DeForest Buckner, isn’t as “polished” but had “a lot of great potential.”

Last year, the 49ers set an NFL record by allowing 100yard rushers in seven straight games and surrendered the sixth-most rushing yards (2,654) since 1990. Armstead missed the final eight games with a shoulder injury he sustained in training camp.

The 49ers will put Earl Mitchell, 29, at nose guard after he signed a four-year, $16 million deal last week. Lynch said the seven-year veteran will help set the tone up front.

“I’m excited about what he’s going to do for Buckner and Armstead,” Lynch said. “... We can tell people run to the football, but when one guy is doing it, you better do it or you’re going to stand out like a sore thumb. That’s what he brings.” Eric Branch is a San Francisco Chronicle staff writer.