SANTA CLARA, Calif. -- The San Francisco 49ers' top two running backs did not practice Wednesday as they dealt with various injury issues.

Running backs Christian McCaffrey (bruised calf) and Elijah Mitchell (groin) sat out Wednesday's session.

Coach Kyle Shanahan said Deebo Samuel (ankle) would sit out Wednesday's session, but the star wide receiver was in uniform for the early portion of practice that was open to media and was a limited participant. 

Left tackle Trent Williams also did not practice on Wednesday, getting his regular day of rest.

While Shanahan made no promises about the trio's availability for Sunday's NFC Championship Game against the Philadelphia Eagles, he expressed confidence that all will be ready to go.

"I expect them to but there's no guarantees, especially with it being the NFC Championship Game," Shanahan said. "I think there's a better chance they'll be ready since there's nothing guaranteed after this. So, hopefully. We'll keep our fingers crossed."

McCaffrey and Mitchell's injuries were first mentioned by Shanahan on Monday. He said then he wasn't expecting either ailment to keep McCaffrey or Mitchell from playing against the Eagles. But in the interest of caution, the Niners' two top backs are sitting out Wednesday.

After the 19-12 NFC divisional-round victory against the Dallas Cowboys, McCaffrey said he was feeling the bruised calf late in the game but he, too, was mostly unconcerned about it.

"I was fighting but made it through," McCaffrey said. "Made it through great. But nothing bad. All good. "

Samuel was a new addition to the injury report on Wednesday. Shanahan indicated Samuel has been dealing with the ankle issue for "a little bit."

For his part Samuel said there's no doubt in his mind he'll be ready to go against the Eagles.

"It's just kind of sore," Samuel said. "We're just being cautious and just trying to get ready for Sunday."

Elsewhere on the injury report, quarterback Jimmy Garoppolo had another X-ray on his broken left foot this week. Shanahan said last week there was an "outside chance" Garoppolo could return to practice this week.

But that will not happen, which means a Garoppolo return would only occur if the Niners advance to the Super Bowl. Elsewhere on the injury report, defensive lineman Charles Omenihu (oblique) and cornerback Ambry Thomas (ankle) were limited participants.