Kyle Shanahan, John Lynch disagree over what to do with No. 3 pick?

The San Francisco 49ers traded up to No. 3 overall in the NFL Draft so they can select a quarterback, but it’s unclear which player they are targeting. That may be because they lack organizational consensus at this point.

In an interview with The Rap with Patrick Meagher on SiriusXM’s Mad Dog Radio this week, Michael Lombardi of The Athletic said he has been told that the 49ers’ brass does not agree on which quarterback the team should pick. More specifically, head coach Kyle Shanahan and general manager John Lynch have different views at the moment.

“Someone told me there is a conversation in the building that Kyle wants X and maybe Lynch wants Y. I’m gonna be very clear here — Kyle is gonna make this pick. It’s in his contract. It’s not a question of he’s just gonna do it because of (his) personality. The Shanahans run the 49ers. Lynch is there to do what he is told to do.”

You can hear the full segment below, with the relevant remarks coming at around 2:50.