Jimmy Garoppolo won’t have much time to prove himself worthy of a major contract with the 49ers this season. (Stan Olszewski/Special to S.F. Examiner)

Jimmy Garoppolo won’t have much time to prove himself worthy of a major contract with the 49ers this season. (Stan Olszewski/Special to S.F. Examiner)

49ers like franchise tag for Jimmy Garoppolo

SANTA CLARA — Before the final minute of Sunday’s game, 49ers fans were increasingly irritated about head coach Kyle Shanahan’s reluctance to play Jimmy Garoppolo. They were eager to see if they had a franchise quarterback on the roster before he hit free agency this offseason.

They were missing a crucial detail: The team will have a franchise tag that it will most likely use to extend its assessment of Garoppolo, who was acquired slightly before the trade deadline.

Before Garoppolo took a few snaps in a blowout loss to the Seattle Seahawks, Shanahan all but confirmed the Niners’ intentions to slap Garoppolo with a franchise tag, which can be used on an unrestricted free agent once per offseason.

“That is the good thing about the franchise tag and that’s what, to me, made it an easier decision to trade for him at the time we did,” Shanahan told KNBR last week.

The designation gives the player a one-year contract for more than the average of the top-five salary of his position. For Garoppolo in 2017, that number should be slightly more than $25 million. (The average — which currently sits at slightly less than $24 million — is calculated in April, which will come after the signings of at least a couple expensive quarterbacks.)

On Monday, Shanahan elaborated on why he expects the 49ers to use the distinction on Garoppolo.

The first-year head coach said he wanted to give Garoppolo — who has made two career starts — a fair chance to prove himself before starting negotiations on a long-term deal. His comments also illuminated how different of a position the 49ers are in from the New England Patriots, Garoppolo’s former team. The Niners can afford an experiment; the Pats wouldn’t spend that much money on a backup quarterback.

“Like, ‘Hey, you have this opportunity to get such a good player. What’s the negative?’ Well, you don’t want to lose him in six weeks or eight weeks. If you have the franchise tag, then you don’t have to ever worry about losing him,” Shanahan said. “You can get there, you can do things the right way, really find out what the guy is.”

He described it as a win-win for both parties.

“I think Jimmy has goals and believes in himself that he can be one of the better quarterbacks in the league. Anyone who feels that way, I would assume, wants to be paid that way, or be paid accordingly,” Shanahan said. “… I think Jimmy wants his best opportunity to prove that to us. I’d like to give that to him. If that happens over a five-game span, a three-game span, then great, let’s do it. If it doesn’t, no big deal.”

But with CJ Beathard banged up with a knee contusion and hip strain, Garoppolo may get a chance to prove himself ahead of the 49ers’ preferred schedule. Shanahan didn’t want to commit to a starting quarterback for the 49ers’ Week 13 matchup at Chicago, but said he would have a good idea by Wednesday.

“To give those guys the best chance to be successful, you want to give them all the reps [in practice], which still isn’t enough reps,” he said. “Any time you split those evenly, it’s kind of a disservice to both.”

Two more to the IR

The 49ers’ crowded injured reserve list will have a couple more names added to it.

Raheem Mostert, a backup running back and special teams dynamo, injured his MCL and will miss the rest of the season.

The same prognosis was given to Erik Magnuson, who sprained his foot early in Sunday’s game.

“I was pretty amazed,” Shanahan said. “Got a lot of respect for that guy for staying out there and battling through that, especially with how short we were at tackles.”

Help is on the way

After hurting his shoulder during the final rep of Thursday’s practice, right tackle Trent Brown was a game-time decision for Sunday’s game against the Seahawks. Shanahan expects him to have the same status ahead of the 49ers’ game against the Bears.

“You never know how those shoulders are going to react,” Shanahan said. “I know he tried and he was hoping that he could, but he just couldn’t go.”

The Niners allowed 13 quarterback hits and three sacks in Brown’s absence.

jpalmer@sfexaminer.comcj beathardjimmy garoppolokyle shanahanNFLSan Francisco 49ers

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