49ers

Confirmed: Harbaugh headed to University of Michigan

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Confirmed: Harbaugh headed to University of Michigan

Coach Jim Harbaugh and the 49ers are parting ways after four seasons, which included three trips to the NFC Championship game and one Super Bowl appearance.

Harbaugh has accepted a job to become the next coach at the University of Michigan, sources confirmed Saturday evening to Comcast SportsNet Bay Area’s Dave Feldman.

The New York Times was first to report the official agreement.

Harbaugh and the 49ers are believed to have reached an agreement to allow Harbaugh to leave after four years of his five-year, $25 million contract. He is expected to be on the sideline Sunday when the 49ers finish their season against the Arizona Cardinals at Levi's Stadium.

Harbaugh is scheduled to be introduced at a press conference Tuesday in Ann Arbor, Michigan. Harbaugh played at Michigan under legendary coach Bo Schembechler from 1982-’86. Recent media reports have placed Harbaugh's contract at six years for as much as $49 million.

Harbaugh, an immensely popular figure for the 49ers’ fan base with his black “SF” fleece and khakis, leaves after returning the organization to prominence. When the 49ers hired Harbaugh in January 2011, the club had not made the playoffs for eight consecutive seasons.

[RELATED: Reports: Michigan reps in Bay Area in pursuit of Harbaugh]

It has been a foregone conclusion for most of the season that Harbaugh would not be back with the 49ers due to irreconcilable personality issues with CEO Jed York, general manager Trent Baalke and team president Paraag Marathe.

In four seasons as 49ers coach, Harbaugh’s teams posted a regular-season record of 43-19-1, entering the season finale Sunday.

“There are a lot of distractions around here -- a lot of distractions,” 49ers tight end Davis told CSNBayArea.com last week. “All season long there were a lot of distractions. But we tried our best to fight through them. Even now, there’s a lot of talk about Harbaugh not being here.”

Speculation that this would be Harbaugh’s final season surrounded the 49ers from the opening week of the season. Amid reports of the 49ers’ eventual parting of ways with Harbaugh, York offered a tepid response via Twitter on October 5, just prior to the home game against the Kansas City Chiefs.

York wrote: “Jim is my coach. We are trying to win a SB, not a personality or popularity contest. Any more questions?”

[RELATED: Jim Harbaugh Michigan gear already for sale]

A day later, York said any reports that the 49ers would fire Harbaugh after the season were “categorically not true,” during an interview on "The Rich Eisen Show.”

“We’re focused on getting back to and winning the Super Bowl,” York said. “That’s really the only thing that’s on anybody’s mind here. I’ve said this all along: I would like for nothing else to be in the worst negotiating position possible with Jim.”

But York did not offer any more football-related comments until the closing moments of the 49ers’ 19-3 loss to the Seattle Seahawks on Thanksgiving night.

“Thank you #49ersfaithful for coming out strong tonight. This performance wasn't acceptable. I apologize for that,” York wrote.

Harbaugh did not directly address York’s comment, but he made it clear exactly how he felt with York’s choice of words.

“It’s our job to move on without excuse, without apology and get it right. Make it right,” Harbaugh said.

But the 49ers could not get it right.

[RATTO: Harbaugh goes for comfort, what's next for coach?]

The loss on Thanksgiving was the beginning of the longest 49ers losing since Harbaugh became coach. After an embarrassing December 7 loss to the Oakland Raiders, who entered the game with just one victory, the 49ers officially fell out of playoff contention with a 17-7 loss at Seattle.

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Afterward, quarterback Colin Kaepernick said it was strange to hear the rampant talk about Harbaugh coaching his final season with the 49ers.

“That’s something I can’t fully wrap my mind around why that would be the situation,” Kaepernick said. “But he has my full support, no matter if he’s here or somewhere else. I hope he’s back here and I think he’s a great coach.”

Harbaugh came to the 49ers as the organization’s 18th head coach after a wildly successful run at Stanford, where he inherited a one-win team and turned the program around to become a national power.

"It's the perfect competitive challenge," Harbaugh said at his introductory press conference with the 49ers. "I look forward to coaching against John Harbaugh, Bill Belichick and the many great coaches in the NFL. That kind of challenge, I willingly accept it and I look very much forward to it."

Late in the 2012 season, Harbaugh’s 49ers defeated Belichick’s New England Patriots. And he met his brother, John Harbaugh, and the Baltimore Ravens in Super Bowl XLVII.

The 49ers rallied from a 28-6 deficit in the third quarter and stood 5 yards from a potential Super Bowl title before three consecutive incomplete passes sent the organization to its first loss in the NFL championship game.

The 49ers made it back to the playoffs in 2013, but were eliminated when Kaepernick’s pass toward Michael Crabtree end the end zone was tipped by Seattle cornerback Richard Sherman and intercepted by linebacker Malcolm Smith with 22 seconds remaining.

York and Harbaugh were unable to work out contract extensions after the past two seasons. Last year, when the Cleveland Browns contacted York about the possibility of swinging a trade for Harbaugh, York called Harbaugh to see if it was something Harbaugh wanted to pursue.

“He wasn’t in the office,” York told Bay Area reporters in March at the NFL owners meeting. “So I talked to him probably an hour after the Browns thing. I called. There was no answer. I texted and said, ‘Hey, give me a ring.’ He was at preschool with (his daughter). ‘Listen, I just want to ask you, was there any interest in your part? This is the phone call I got.’ “

Harbaugh called him back and said, according to York, “I don’t know what you’re talking about.”

“And that was the end of it,” York said.

The sides announced at the beginning of training camp that they would table contract talks until the end of the season – in essence, making this a make-or-break season. But the 49ers struggled on the field and off the field.

Tight end Vernon Davis and guard Alex Boone did not take part in the team’s offseason program due to contract issues, prompting Harbaugh to say, “(It’s) not the decision I envision being the 49er way.”

Defensive end Ray McDonald was arrested for alleged domestic violence before the 49ers’ first game. The organization cited “due process” while keeping McDonald active and playing during the investigation. When McDonald was investigated again as a suspect in an alleged sexual assault on Dec. 17, the 49ers released him later that day.

The 49ers experienced an injury-riddled season in which 18 players finished the year on injured reserve, including linebackers Patrick Willis, NaVorro Bowman and Chris Borland, and nose tackles Ian Williams and Glenn Dorsey, center Daniel Kilgore, tight end Vance McDonald, and first-round draft pick Jimmie Ward.

Harbaugh never talked about his other coaching options, which included the possibility he could remain in the NFL.

“What will happen, will happen,” Harbaugh said at his Monday press conference. “What won’t happen, won’t happen. I work at the pleasure of the organization and I will let them have the floor on that.”  

Snap count: 49ers' rookie running backs watch the veterans

Snap count: 49ers' rookie running backs watch the veterans

SANTA CLARA – Rookie running backs Joe Williams and Matt Breida have made strong bids for roster spots. But on Saturday night, the 49ers wanted to see what the veterans could do.

Williams entered the game late and played only four snaps of offense. He carried once for 1 yard. Another designed run play was aborted when a Denver Broncos defensive lineman got into the backfield so quickly he forced a fumble before the handoff could occur.

Breida, an undrafted rookie from Georgia Southern, did not see any snaps on offense in the 49ers’ 33-14 loss to the Denver Broncos at Levi’s Stadium.

Coach Kyle Shanahan said the plan all along was for Tim Hightower and Kapri Bibbs to see a lot of action after neither played in the exhibition opener.

“We’re trying to give them a chance to compete,” Shanahan said. “We see it in practice each day, but in games you want to see what guys do breaking through those arm tackles and see how they perform.

“We have a tough competition at back. If you rotate them every series, you don’t really give anyone a chance to show what they are. We try to do it that way. I’ve really tried to do it that way my entire career. You try to select which games you’re going to try to give guys a number of carries, so you have enough when it’s all said and done after four to try to make a decision.”

The 49ers’ run game was non-existent against the Broncos. Starter Carlos Hyde gained 26 yards on eight attempts. Bibbs managed 6 yards on four carries, while Hightower was thrown for minus-1 yard on three rushes.

In the exhibition opener last week against the Kansas City Chiefs, Williams gained 60 yards on seven carries, while Breida rushed for 40 yards on 11 tries. Raheem Mostert, the 49ers' leading rusher (15 carries, 89 yards) in the exhibition opener, was limited to just four plays on special teams.

Here is a look at the 49ers’ playing time on offense, defense and special teams:

OFFENSE
Quarterback – *Brian Hoyer 24, C.J. Beathard 20, Matt Barkley 4
Running back – *Carlos Hyde 20, Tim Hightower 14, Kapri Bibbs 10, *Kyle Juszczyk 6, Tyler McCloskey 5, Joe Williams 4
Wide receiver – Louis Murphy 23, *Marquise Goodwin 18, Kendrick Bourne 15, Jeremy Kerley 13, Aldrick Robinson 13, Victor Bolden 12, Trent Taylor 11, *Pierre Garçon 10, DeAndre Carter 5
Tight end – George Kittle 22, Garrett Celek 12, Logan Paulsen 10, *Vance McDonald 9, Blake Bell 5, Cole Hikutini 3
Offensive line – Erik Magnuson 25, *Trent Brown 24, *Zane Beadles 23, *Daniel Kilgore 23, *Brandon Fusco 23, *Joe Staley 23, JP Flynn 21, Tim Barnes 21, Garry Gilliam 21, John Theus 20, Darrell Williams 4, Norman Price 4, Andrew Lauderdale 4, Andrew Gardner 4

DEFENSE
Defensive line – D.J. Jones 38, Leger Douzable 36, Pita Taumoepenu 31, *Chris Jones 30, Quinton Dial 23, *Arik Armstead 23, *Earl Mitchell 19, Solomon Thomas 16, *Tank Carradine 15, Noble Nwachukwu 15, Elvis Dumervil 8
Linebacker – Dekoda Watson 33, Brock Coyle 30, Ray-Ray Armstrong 30, Ahmad Brooks 30, *Eli Harold 23, *Reuben Foster 23, *NaVorro Bowman 23, Shayne Skov 22, Alex Calitro 21
Cornerback – Asa Jackson 40, Ahkello Witherspoon 39, Keith Reaser 30, Will Davis 22, *Dontae Johnson 20, *Rashard Robinson 20, K’Waun Williams 11
Safety – *Lorenzo Jerome 37, Jaquiski Tartt 33, *Eric Reid 23, Don Jones 22, Vinnie Sunseri 19, Adrian Colbert 19
* -- Starter

SPECIAL TEAMS
D.Jones 18, Bell 17, Taumoepenu 17, DeAndre Smelter 16, Jerome 16, Celek 11, Watson 11, Coyle 10, Sunseri 10, Armstrong 10, Skov 9, C.Jones 9, Tartt 9, Bradley Pinion 8, Calitro 8, Colbert 8, Paulsen 8, Jackson 8, Kyle Nelson 7, Bolden 7, Bibbs 6, Witherspoon 6, Reaser 5, Dial 5, Davis 5, Raheem Mostert 4, Harold 4, Carter 4, Johnson 4, D.Williams 4, D.J. Jones 4, Robbie Gould 3, Robinson 3, J.Williams 3, Flynn 3, Douzable 3, Carradine 3, Nwachukwu 2, Price 2, Taylor 2, Kerley 2, Barnes 2, Theus 2, Magnuson 2, McCloskey 2, Armstrong 2, Foster 2, Reid 2, Bowman 2, Mitchell 2, Nick Rose 1, Matt Breida 1, Tim Patrick 1, Thomas 1, Bourne 1, Lauderdale 1, Brooks 1

DID NOT PLAY
QB Nick Mullens, WR Aaron Burbridge, DB Will Redmond, DB Jimmie Ward, DB Prince Charles Iworah, LB Sean Porter, LB Aaron Lynch, G Joshua Garnett, DL Ronald Blair, DL DeForest Buckner

Potential big play slips from Hoyer's grasp during preseason loss to Broncos

Potential big play slips from Hoyer's grasp during preseason loss to Broncos

SANTA CLARA – Quarterback Brian Hoyer threw the ball well enough to impress the Denver Broncos’ defensive backs during the 49ers’ two joint practices.

While he hit most of his passes on Saturday night, it was one that slipped away that summarized the 49ers’ 33-14 loss to the Broncos in the second exhibition game for both teams.

Hoyer had plenty of time to throw and saw a potential big play unfolding as he started to throw to wide receiver Jeremy Kerley. But the ball popped out of Hoyer’s right hand as he began to throw.

“I was getting ready to rip it to Kerley,” Hoyer said. “He had a double-move route, and I thought he was going to win. I went to throw it. And I was going to throw it hard, and literally, I think my arm even went forward and I was looking around, ‘What happened to the ball?' "

The ball ended up loose on the ground, where Broncos defensive lineman Shelby Harris recovered.

“My quarterbacks coach asked me, ‘When’s the last time that happened to you?’ Hoyer said. “Maybe a few years ago in practice, that happened one time. I never had that happen in a game. It’s the worst feeling. You go to throw the ball and you’re looking, and all of a sudden, you look around and you have no idea where it is.”

Hoyer and the 49ers passing game was sharp during two practice sessions with the Broncos during the week, prompting All-Pro defensive backs Aqib Talib and Chris Harris to praise the Hoyer, as well as coach Kyle Shanahan's offense.

Hoyer completed 8 of 11 pass attempts for 89 yards under the lights of Levi's Stadium. He threw an interception when 49ers receiver Marquise Goodwin juggled the ball and Denver defensive back Chris Lewis-Harris wrestled the ball away from him as they tumbled to the ground.

“There weren’t any reads on his 11 attempts that I was upset with,” Shanahan said of Hoyer.

“(On) his pick, Marquise has to catch that ball. He threw it to him. That keeps the drive alive. He just didn’t catch it clean and the DB made a good play. I wish Brian could’ve played longer to get a chance to get into some sort of rhythm.”

In the game, the 49ers committed 11 penalties for 86 yards and turned the ball over five times. Denver scored 27 points off those turnovers.

“I don’t think any of us should be pleased right now,” Hoyer said. “When you put the defense in that situation, regardless of whether it’s a regular-season game or a preseason game, you should feel displeased with the performance.”