49ers wide open at quarterback after Kaepernick opts out

Over the past three seasons, the 49ers roster has resembled a block of swiss cheese.

Retirements, off-the-field issues and injuries have punched holes in San Francisco depth charts like crude oil drillers on the bottom of the Pacific Ocean.

Wednesday morning, Ian Rapaport of NFL Network reported San Francisco will have one more hole to address, as Colin Kaepernick — who started 11 regular season games for San Francisco in the 2016-17 season — will exercise the opt-out-clause of his contract making him a free agent.

The move will save the 49ers $14.5 million in cap space, according to Tim Daniels of Bleacher Report, but will still cost the team $4.9 million on their books due to a “dead cap hit” from Kaepernick’s earlier signing bonus.

Kaepernick, who led the 49ers to consecutive NFC championship games and a Super Bowl in 2013, had a workman-like season in 2016, completing 59.2 percent of his passes for more than 2,200 yards in 11 starts.

What are the 49ers’ options at QB?

The most obvious option would be to re-evaluate Blaine Gabbert, Thad Lewis and Christian Ponder, all set to become free agents within a week, per Adam Stites of SBNation. Gabbert started the first five games for the 49ers last season, and will be on top of that list.

49ers head coach Kyle Shanahan said Wednesday at the NFL Scouting Combine via Matt Maiocco of CSN Bay Area:

“We don’t have anybody on our roster, so I throw them all in the category of everybody else who’s a free agent and the possibilities going into the draft.”

Considering yesterday’s news regarding what was thought to be a potential trade with the Washington Redskins for signal caller Kirk Cousins — in which Washington quickly shut down discussions — the idea of potential trades may be tough.

Even after Cousins stated publicly he would like to play for his former offensive coordinator in Shanahan, the Redskins quickly placed a franchise tag on their QB and halted all trade rumors, per Ian Rapaport of NFL Network.

Soon-to-be free agent Tony Romo of the Cowboys has also been publicly shopped to a team of his choice but has yet to publicly express interest in San Francisco due to the fact that they aren’t an immediate contender for a Lombardi trophy. Instead Romo has expressed interest in joining a team like the Denver Broncos who won the Super Bowl only two season ago according to Ian Rapoport.

Who can San Francisco target in the draft?

The only other option comes from the No. 2 overall pick in the upcoming 2017 Draft.

Draft experts have graded three quarterbacks at the top of their position in the 2017 draft class: Mitch Trubisky out of North Carolina, DeShone Kizer from Notre Dame and Deshaun Watson out of Clemson.

Draft experts Dane Brugler, Pete Prisco, Will Brinson and Jared Dubin, [[LINK]] all of CBS Sports, have Trubisky listed as the No. 2 overall pick going to San Francisco in  mock drafts posted on Wednesday.

A common argument against choosing a quarterback in the first round is 49ers recent history.

In 2005, San Francisco famously took Alex Smith out of Utah with the No. 1 overall pick. Smith’s career would be less than satisfactory until Jim Harbaugh arrived in 2011, rejuvenating Smith’s career.

With the NFL combine underway in Indianapolis this week, the evaluation process at quarterback will continue as Shanahan and company prepare for their inaugural season in San Francisco.