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Could Kyle Shanahan’s stock have gone down in Jed York’s eyes on Sunday?

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The 49ers have a new coach—could he already started on a bad note?

No denying that the San Francisco 49ers had to hire a head coach, and Kyle Shanahan was the obvious choice. The 49ers’ “process” if you call it led to the organization being the last one in the head coaching race. Obviously, looking for a general manager that would work with the coach slowed things down, but the 49ers had little decisions elsewhere that would be considered smart.

What’s interesting is what happened in the Super Bowl on Sunday. Shanahan has come under heavy scrutiny for his play-calling in the second half and even shouldered the blame of the loss. Regardless of who is at fault—the way this game went down felt very similar to the way the San Francisco 49ers lost Super Bowl 47 against the Baltimore Ravens a game that had then-head coach Jim Harbaugh and offensive coordinator Greg Roman stumbling on the goal line. Burning a crucial timeout and neglecting to get Frank Gore in the game, the 49ers Super Bowl chance ended on a Colin Kaepernick lolipopped ball into the air. And since he’s not Tom Brady, he’s not getting a pass interference or defensive holding flag to decide the game.

This is being brought up because that was the beginning of the end for Jim Harbaugh. After losing the NFC Championship game the following season, the drama of Jim Harbaugh’s departure began. Most of this stemmed from Reports that Jed York thought Jim Tomsula of all people could have won with the roster the 49ers had at the time. There is some speculation that a lot of that could have been former general manager Trent Baalke whispering in York’s ear, but whatever report or rumor you want to believe—the end of the Super Bowl 47 marked the beginning of the end of York’s faith in Harbaugh.

Which brings us to Kyle Shanahan. No doubt, Jed York saw the Falcons collapse on Sunday, and there was little choice to hire Shanahan regardless of his performance. Shanahan got the reported six-year deal tying him to the hip of newly hired 49ers general manager John Lynch, but how much faith does the 49ers front office have in Shanahan after the Super Bowl? If this is a culture of winning Super Bowls and anything less is unacceptable, Shanahan might begin this contract in a nicely dug hole. Let’s not keep saying how cheap the Yorks are when it comes to head coaches—when the coaching search began, they were paying multiple head coaches to not coach. If you think they’d keep Shanahan the full six years if there’s nothing but mediocrity seeping from the building, you’re kidding yourself.

Reports say York will have little to do with football operations. He’s leaving it to Lynch and Shanahan...and Paraag Marathe. There’s a different emotion involved when you’re watching your new coach’s former team flame out as opposed to the team you own, so perhaps Sunday’s episode wasn’t even familiar to the 49ers top brass.

There’s a lot of reason to believe York has learned a lot about expectations and can’t hold the end of the Super Bowl over Kyle Shanahan’s head. Or maybe faith in Kyle Shanahan has already gone down a few notches. We won’t get an answer, but hopefully York has learned something.