With Colin Kaepernick headed toward free agency, 49ers begin anew at QB

Kaepernick's opt-out was expected (1:50)

Adam Schefter, Mark Dominik and Louis Riddick react to Colin Kaepernick opting out of his contract with the 49ers and examine what is next for Kaepernick and San Francisco. (1:50)

SANTA CLARA, Calif. -- From the moment quarterback Colin Kaepernick signed a reworked deal with the San Francisco 49ers that allowed him to opt out of the final year, there was never any doubt that he was going to take advantage.

Now that Kaepernick and his new representatives have informed all 32 NFL teams that he will be testing free agency for the first time in his career, we no longer have to deal in hypotheticals. Kaepernick will examine all options for his next NFL home.

For the 49ers and coach Kyle Shanahan, the quarterback search is officially on. With Kaepernick set to opt out, the Niners no longer have a single quarterback under contract for 2017. When free agency begins on March 9, Kaepernick will join Blaine Gabbert, Thad Lewis and Christian Ponder as 2016 Niners quarterbacks on the market.

With Shanahan and general manager John Lynch in place, there's a real chance that none of those quarterbacks return to San Francisco. None of them have experience in Shanahan's system and it's fair to wonder whether any of them fit the mold of what Shanahan is looking for at the position. It's worth noting Kaepernick is open to a return to the Niners, though it would have to come at a reduced price and probably isn't an option until he examines other possibilities.

Although Shanahan has had success at various NFL stops with different types of quarterbacks, he hasn't always had a major say in who his quarterback was going to be. Now, as a first-year head coach, Shanahan will be able to have ultimate input in what the 49ers' quarterback room will look like.

That could mean making a trade and signing two free agents. It could mean signing three free agents. It could mean a free agent and two draft picks. The permutations are many but regardless of how it plays out, the first order of business for Shanahan is finding at least one quarterback who represents an upgrade over Kaepernick.

If indeed the Niners and Kaepernick's relationship has come to an end, it's incumbent on the 49ers to do better. That's true of any position when you allow a player to leave but especially at quarterback. On the surface, a look at Kaepernick's recent production might indicate that finding someone better shouldn't be that difficult, but it's not that simple.

In 2016, Kaepernick started 11 games and had his best statistical season since 2013. The 49ers were just 1-10 in his starts, but his 90.7 passer rating was his best in three years and put him at No. 17 among quarterbacks in the league. In itself, that production is middle of the pack, but it was still a dramatic improvement over 2015 when he was 31st. He also had the sixth best touchdown to interception ratio in the league and was first among quarterbacks in yards per carry.

That's not to say there wasn't room for improvement, but it was still better than a chunk of the other starting signal-callers around the league. So, as the Niners' search for quarterback solutions marches on, that performance should serve as a baseline for what the Niners hope to get from their next starter.

With Washington placing the exclusive franchise tag on Kirk Cousins on Tuesday, that option seems to be off the table, at least for this year, barring the type of outrageous trade offer the 49ers are unlikely to make. Wednesday also brought the news that the New England Patriots intend to hold on to Jimmy Garoppolo rather than trade him, thus removing another potential immediate option.

So, where do the 49ers go from here? Veteran Matt Schaub, who worked with Shanahan in Houston and Atlanta, seems like the likeliest option as a veteran who can help install Shanahan's offense and serve as a backup or even a short-term starter in a pinch. Schaub is also set to be a free agent on March 9.

Other quarterbacks expected to be available include Chicago's Jay Cutler and Brian Hoyer and Tampa Bay's Mike Glennon. Like Schaub, Hoyer has experience in Shanahan's offense from their time together in Cleveland. None are likely to be a long-term answer, but we already know the Niners are willing to be patient to find that guy.

This week, Shanahan and Co. are in Indianapolis with the rest of the NFL world getting a closer look at this year's crop of draft prospects. There's no doubt quarterbacks like North Carolina's Mitch Trubisky, Clemson's Deshaun Watson, Notre Dame's DeShone Kizer, Texas Tech's Patrick Mahomes and others will garner much of the team's attention over the next few days.

As is always the case with draft prospects, there are no sure things. But if nothing else, with a clean quarterback slate in front of him, Shanahan can take the canvas and make it look however he wants -- with or without Kaepernick.