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The good news is that Trey Lance might be available to back up Garoppolo. Shanahan expects the rookie to practice this week.
"Coming back from the injury, they tell me he's on pace to be able to come out to practice on Wednesday," Shanahan said. "He might be a little limited at it, though, but that's what we're hoping for.
"But in terms of deciding who's going at quarterback, that has to do with Jimmy's health. Jimmy, I wanted to see how his calf was. It was good today, and so he'll be starting.
"Hopefully, Trey will get back in practice and have a good enough week to where he can dress. If Trey ends up dressing, then there's always a good chance that he'll end up getting some plays in there."
Garoppolo, coming off a calf injury, started against the Colts and completed 16 of his 27 pass attempts for 181 yards with a touchdown, two interceptions, and was sacked twice in the 49ers' 30-18 loss. Shanahan added that Garoppolo's job was never on the line this past weekend.
"We didn't go into that game thinking that Jimmy was one bad game away from losing his job or anything like that," Shanahan said. "Jimmy didn't play as good as he could, which he knows that [and] I know that. Also, I think it was some pretty hard circumstances for him, for both quarterbacks, considering some of the weather. But I definitely thought he could have played better. But that was not a game to where, 'Hey, if Jimmy has one bad game, he's losing his job.'
"We know Trey's the future here, and [we're] trying to do what's best for him and our team, and Trey's coming off a pretty big injury. And we're going to keep bringing him along, and keep getting him prepared as good as he can be to always be ready to come in and help on the plays that we asked him to do, always be ready to take over if Jimmy gets hurt, and being ready to be the future for us too."
Later, Shanahan was asked when he might opt to play Lance over Garoppolo. When does that conversation come into play?
"Our record is 2-4, and we've lost four in a row, so I get why I'm getting questions like that. But we're 2-4. You get two games in a row, and you're right back to .500, and you've got a chance. ... I get all the questions, but it's way too early for me to start thinking about just getting guys experience and giving up on the year in that way.
"I'm trying to do what's best for our team, and also what's best for those players, not just Trey, but other guys. Getting experience just to get it isn't always beneficial."
Shanahan acknowledged that Garoppolo's Week 7 outing wasn't great but feels the veteran quarterback has done enough to warrant being the 49ers' starter this season.
"I thought Jimmy had his worst game yesterday," Shanahan said. "I thought Jimmy's done some good things in the three-and-a-half games that he's played. If you remember, I thought he did some pretty good things in our first game, getting us up to a 41-17 lead [against the Lions]. I think he came back and made some unbelievable plays to give us the lead with 30 seconds left versus Green Bay on Sunday Night Football, which, minus two unbelievable plays from Aaron [Rodgers], I thought he did what a good quarterback should do, leading you down there, and getting a big score on a number of passes.