Shanahan already made his statement regarding the report when he called it "complete bulls--t" in a text sent to NBC Sports Bay Area. Friday was Lynch's turn to provide a lengthier response to the report.
"It's nonsense," Lynch said on the "Joe, Lo and Dibs" show. "Look, I'm a big boy. Kyle's a big boy. People can talk about a lot of things; whether they like our pick. People can say, 'Hey, you guys are dumb for taking a punter in the fourth round. We've got big shoulders. We're going to do what we think is right for this organization. We're proud of what we've done.
"But the notion that we're not working together couldn't be further from the truth. We have a tremendous working relationship. We're great friends off the field. There's a lot of trust. We came in this together. We came in knowing there would be some tough times, and it wasn't going to be easy, but it was going to be worth it.
"I can tell Niner fans that we're strong as ever, and there's a lot of trust and faith. I feel so great for this organization that they've got Kyle Shanahan, a tremendous leader, tremendous mind. Our players love him. I love him. We've got each other's back, and that's all that I'll say on that because that's just the truth."
Miller's report indicated that there was some conflict in the 49ers' draft room last week. It was an alleged conflict that led the Bleacher Report analyst to speculate that a split might be in the duo's future.
Lynch went on to say that he and Shanahan work together when drafting players or bringing in players via free agency. However, the two might now always agree on a player.
"It's Kyle's job if he likes the player and I'm not sure, to get me off the fence, and say, 'Here's why I like him,'" Lynch said. "Then there's plenty of opportunities where I like a player, and he's not quite there, and then I make tapes. We work like that together.
"Fortunately, most of the time, and this is what drew us together through my broadcasts and his games, our eyes happen to see the same things on a lot of occasions. Most of the time, we're seeing the same thing. But I can tell you, by the time we've brought a player in here, we're both on board."
You can listen to the entire interview with Lynch below.
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