SANTA CLARA — John Lynch came out of his first draft as an NFL general manager with two of the top three players on San Francisco’s board and a couple of extra picks to boot.

The rookie general manager would have had a hard time scripting the day any better. He traded down one spot to No. 3 to get Stanford defensive lineman Solomon Thomas and then packaged one of the extra picks from that deal with his own second-rounder to get Alabama linebacker Reuben Foster at 31.

“We got two of our top three players,” Lynch said. “We’re thrilled. We’re ecstatic. We think these guys have traits that encompass what we want to be about as a football organization.”

The trading started when Chicago wanted to move up one spot to select quarterback Mitchell Trubisky. With other teams interested in that pick, the Niners were able to get extra picks in the third and fourth round this year and a 2018 third-rounder and still draft their second-highest rated player in Thomas.

“There were other people involved,” Lynch said. “The trade improved the last day because of that.”

Then when Foster started slipping possibly because of concerns about his injured shoulder and off-field character issues, San Francisco started making calls midway through the round to get an additional first-round pick.

They were finally able to move from 34th to 31st by sending the fourth-round pick acquired from Chicago to Seattle and added the Butkus Award winner to their defense. Coach Kyle Shanahan said Foster’s play jumped off the film every time he studied Alabama’s defense.

“No matter who I was studying and watching, No. 10 was flying around passing everybody up,” Shanahan said. “No matter who I studied. I had a hard time not watching No. 10, which was Reuben. The way he plays, the way he hits, the way he runs, that’s why you want him on your team.”

But Foster was hurt by a shoulder injury that he said should be fully healed by training camp, as well as off-field issues. Foster was kicked out of the combine over a confrontation with a hospital worker and had a diluted drug test sample, turning him from a projected top 10 pick to one that almost didn’t make it in the first round.

“They gave me a chance,” Foster said. “I really appreciate the 49ers. I’m ready to go hard and work hard and prove I’m worthy of the spot. They’re not going to regret it.”

The 49ers sent VP of football affairs Keena Turner and team pastor Earl Smith to Alabama to meet with Foster and came away convinced that he was not a character risk.

There were no off-field questions surrounding Thomas, who was the third straight defensive lineman taken with San Francisco’s top pick, following Arik Armstead in 2015 and DeForest Buckner last year.

Lynch, as a Stanford graduate, is quite familiar with Thomas. He has spent time around the program in recent years and even took a class on decision-making with Thomas where they collaborated on a project.

“I was star struck the first day of class,” Thomas said. “I tried to cling on to him, learn from him. It was a really cool experience to be in class with him.”

Thomas said the two kept in touch since then and now he wants to make Lynch proud as his first draft pick ever as a general manager.

Thomas has the versatility to play outside on the base defense where he is an elite run stopper and inside as a pass rusher in nickel situations. He had eight sacks and 15 tackles for loss last season at Stanford when he was named the top defensive lineman in the Pac-12.

Thomas has been compared to Seattle defensive end Michael Bennett and is expected to play a similar role in San Francisco under coordinator Robert Saleh, a former assistant for the Seahawks.

“We’re both very versatile,” Thomas said. “We’re quick. But I have to earn my stripes before I even get compared to him. I have to play my first down, earn my stripes from my teammates and earn their respect. That’s what I’m trying to do right now.”

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