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Joe Williams was off the 49ers draft board the night before team selected

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This anecdote tells us so much about the dynamic between John Lynch and Kyle Shanahan.

The decision to select quarterback C.J. Beathard was a big surprise for 49ers fans, but the biggest surprise within the organization proved to be the decision to select Utah running back Joe Williams.

When John Lynch and Kyle Shanahan took over the San Francisco 49ers front office and coaching staff, they repeatedly talked about football character. They talked about wanting players committed to football and the team. MMQB’s Peter King was embedded with the team during draft week, and he mentioned various traits the 49ers were looking at with each pick. Football passion and dependability were high on the list.

While Williams was an incredibly talented running back, he departed the Utah football team last September, citing mental exhaustion. John Lynch said over the weekend that when the 49ers were assessing their draft board, they removed Williams because of the belief that he had “quit” on his team.

It turns out there was so much more to it. In his post-draft conference call, Williams explained some of the many issues. His sister died ten years ago, and Williams had blamed himself because he had fallen asleep with her in his arms before she passed. He blamed himself, and according to King, that carried with him over the past decade. He was diagnosed last year with manic depression, and he approached Utah head coach Kyle Whittingham and told his coach he would do more harm than good staying on the team. They agreed that he would step away to work on his own issues.

Eventually, injuries mounted and Whittingham and Williams spoke. Williams decided to return to the team and showed off his incredible talent, rushing for 179 yards against Oregon State, and then 332 yards and four touchdowns in a win over UCLA.

None of the background issues were known to the 49ers in the weeks leading up to the draft. Kyle Shanahan remained enamored by his talent, and on Friday, was hoping the 49ers would be able to land him on Saturday. He discussed it with John Lynch, and made it clear how much he coveted Williams’ talent.

Lynch remained concerned about Williams’ decision to leave the Utah football team, and so he spoke with Kyle Whittingham, and then had a 30 minute call with Williams. He realized the background to the decision, and after another quick look at the tape, told Peter king, they needed to get him.

“Screw it,” he said to himself Saturday morning. “I’m going to try to jump up and get this guy.”

The 49ers dealt their fourth (No. 143) and fifth (No. 161) round picks to the Indianapolis Colts and moved up to No. 121. They had the running back Williams coveted in a big way. How badly did Shanahan want him? He told King, “I’m telling you right now: If we don’t get him, I’ll be sick. I will be contemplating Joe Williams all night.”

The Williams story is a fascinating one, but this also offers a really great perspective on the dynamic between John Lynch and Kyle Shanahan. We don’t know how this would have played out under Trent Baalke, or any other GM/HC combination, but this gives us further reason for optimism about the 49ers new GM and head coach. It shows that Lynch is willing to re-consider his opinions, rather than holding fast and refusing to change his mind. It shows that Lynch and Shanahan already have the kind of trust that is critical for rebuilding the organization.