AP

As it turns out, coach Jim Harbaugh is a bargain in comparison to quarterback Colin Kaepernick.

At a time when it’s believed that Harbaugh hopes to increase his annual salary from $5 million to $6.5 million in 2014, Kaepernick hopes to end in a much higher spot. While starting in a much lower one.

Due to earn $973,000 this year, Kaepernick reportedly is looking for $18 million per year as part of a long-term deal, according to Ben Volin of the Boston Globe.

That would put Kaepernick in the same ballpark as Bears quarterback Jay Cutler and Cowboys quarterback Tony Romo, and slightly ahead of Lions quarterback Matthew Stafford, who averages $17.6 million per year.

It’s also considerably more than Patriots quarterback Tom Brady’s current $14.1 million per year deal, which nevertheless kicked off in 2013 with a $30 million signing bonus.

The question for the 49ers is whether to take the Joe Flacco approach or the Matt Ryan approach. In 2012, the Ravens opted to let Flacco finish his rookie contract, and he did so with a Super Bowl MVP trophy. It backed the Ravens into a corner, forcing them to choose between making him the highest-paid quarterback in the league or starting down a year-to-year path under the exclusive franchise tag that would have given him more than $80 million in three years.

In 2013, the Falcons opted to pay Matt Ryan before he completed the final year of his rookie deal and backed the team into the same corner, forcing Atlanta to break the bank even bigger in early 2014. Despite the team’s unexpectedly bad season, the Falcons still would have been faced with a dilemma between using the non-exclusive franchise tag (and risking a pilfering by another team happy to give up two first-round picks) and applying the exclusive version of the tag.

Kaepernick arguably hasn’t played enough games (he has only 23 regular-season starts) to justify the kind of money he wants. Also, given his mobile playing style, the 49ers will assume a greater injury risk upon giving Kaepernick long-term security.

With new team president Paraag Marathe, an analytics aficionado, recently explaining at the MIT Sloan Sports Analytics Conference that advanced statistics “absolutely play a big role” in contract negotiations, the sample size is still too small to pay Kaepernick at or near the top of the market.

“Both sides in a contract negotiation, both sides are using analytics and data to help support — it’s confirmation bias to the max, everybody’s trying to find evidence that supports whatever theory or contract demand they want to make,” Marathe said, via Mike Rodak of ESPN.com. “They can cut it and slice it in a lot of ways that help you.”

Two stats can slice apart the legend of Colin Kaepernick. As explained in the latest edition of ESPN The Magazine, Kaepernick had a league-worst 54.6 completion percentage while under pressure. He also was sacked 20.2 percent of the time when facing pressure, the fourth highest average among all NFL starters.

Then there’s the question of whether Kaepernick’s success comes more from his innate abilities or from the highly talented team that surrounds him. And whether any other coach can get out of Kaepernick the production that Harbaugh has — especially once the postseason rolls around and Kaepernick seems to find a higher level of play.

With the Harbaugh situation potentially imploding after 2014, it’s probably a good idea to wait to pay Kaepernick the kind of money he’s looking for. If he has another strong season, the number won’t get much higher in 2015. If Kaepernick struggles, it could become a lot cheaper to keep him.