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SANTA CLARA — Wednesday afternoon, Jimmy Garoppolo practiced for the first time as the 49ers’ starting quarterback.

Garoppolo took every rep with the starters. Practice-squad quarterback Nick Mullens played with the scout team. And former starter C.J. Beathard watched from the sideline with a bruised left knee and strained hip. He did not participate in drills.

Earlier in the afternoon, head coach Kyle Shanahan explained his reasoning for making the switch from Beathard to Garoppolo this week.

“It’s a decision we’ve had to look into each week,” Shanahan said in the 49ers auditorium. “It definitely hasn’t been an easy decision. I’ve wanted to get a chance to see Jimmy play. I’ve also wanted a chance to let C.J. continue to play.

“So we’ve been trying to balance that out, and also give Jimmy a chance to fully get ready. The longer you wait, the more ready he will be. He won’t fully be there, I believe, until next year. But with everything going the way it did, also with C.J. being not able to practice today and maybe not throughout the week, that made the decision a little bit easier.”

Would Shanahan’s decision have been different if Beathard were healthy?

“I don’t know,” Shanahan said. “I can’t really speak to a hypothetical. I knew it was going to be a tough decision anyway, but this made it a lot easier.”

Shanahan said he expects Beathard will be a limited participant during today’s and Friday’s practices. Beathard said he expects to be healthy enough to suit up Sunday and back up Garoppolo. “Unless I just don’t get any better at all this week,” Beathard said. “I’m sure I’ll be ready.”

Beathard suffered injuries to his left leg last Sunday when he got hit by Seattle Seahawks defensive end Michael Bennett. On that play, Bennett beat 49ers backup right tackle Erik Magnuson, who was filling in for starter Trent Brown. Brown injured his shoulder during practice last week. This week, the 49ers placed Magnuson on IR with a sprained foot.

Will Brown return to the lineup this Sunday and protect Garoppolo when the 49ers play the Chicago Bears?

“Not necessarily,” Shanahan said. “(Brown) is not going to practice today, so I’m still not sure on that.”

If Brown can’t go, backup center Zane Beadles would start for him at right tackle. So Garoppolo may play behind a patched-together offensive line.

The 49ers traded for Garoppolo one month ago today. While he continues to learn the 49ers offense, he must now learn the upcoming opponent’s defense at the same time.

“That has been the tricky part the last couple weeks,” Garoppolo said. “I’ve kind of gotten into a little bit of a routine with that. I know I was the backup for the last couple weeks, but you still prepare as if you’re the starter. So, learning the other team’s defense, watching as much film as you can while still (learning the 49ers offense). There are things that we’ll put in and I’ll learn for the first time. That part of the learning curve I’m pretty comfortable with now.”

Garoppolo works closely with center Daniel Kilgore, who evaluated what Garoppolo brings to the 49ers.

“He is a guy who has been in the league for three, four years now. He has been on a winning team. He has backed up Tom Brady his whole career. I’d say there is a level of excitement. But ultimately he’s got to go out there and be productive.”

Kilgore assessed Garoppolo’s comfort level with being the quarterback for the 49ers.

“Out of 10, I would say a six or seven (in terms of how comfortable Garoppolo is). He’s still trying to learn, still trying to get the timing down with these receivers. Still learning from Coach Shanahan. He definitely feels better since Day 1, but I would think that he still feels like he has a lot of room to grow.”

Shanahan said Garoppolo doesn’t yet know the entire offense, but knows enough to function Sunday against the Chicago Bears.

“The playbook is this week,” Shanahan said. “It’s not like a big inventory of our training-camp and OTAs system. It’s, ‘What’s our game plan to beat Chicago?’ We put that in Monday night and Tuesday with the idea that we knew we were going to go with Jimmy.

“So when we did that, we put in a game plan that we thought he could do. By no means has he repped it all. That’s what starts today. We just did it in walkthrough. But this game plan is for Jimmy. He’ll work at it all week, and whatever he doesn’t feel comfortable with and he doesn’t get down after he practices, then we’ll take it out. Whatever we go in with Sunday, he’ll know 100 percent of it.”

Shanahan said he will decide week to week which quarterback to start, Garoppolo or Beathard. But if Garoppolo remains healthy and plays well, Shanahan said he probably will start the rest of the season.

“That makes the most sense. I just feel we’re in a situation where I don’t have to make any big commitment like that. I’m not going to speak in any absolutes. We’ll see how this week goes, then we’ll see come Monday what’s the best thing for Jimmy, what’s the best thing for the organization.”

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