The San Francisco 49ers look worse under Chip Kelly than they did a year ago under Jim Tomsula, and that’s a major cause for concern. San Francisco didn’t suffer any significant losses in the offseason, but Kelly’s 49ers are just 1-9 and look less prepared than they did with Tomsula, who was fired for having his 49ers looking consistently unprepared.

Recently, Kelly was asked about his job security and if the 49ers have done anything to convince him that his job is safe going into 2017. His answer was concerning.

“We haven’t had any conversations about that at all and about anybody’s job security,” Kelly said.

Kelly insinuated that he was auditioning for his job for the remainder of this season, telling a reporter he had a “performance review” coming up.

It’s worrying not because Kelly is a great coach and not because the 49ers need some modicum of stability, but more that it would only be a half-step to remove Kelly. One thing that’s become clear is that it goes far beyond the head coach.

It goes up to Jed York, but short of somehow convincing his parents to sell the team, 49ers fans are stuck with him. But they don’t have to be stuck with general manager Trent Baalke, the once-respected executive who is now known less for his gutsy ability to go out and draft an unheralded prospect, and more for some kind of fetish for torn ACLs and being notoriously difficult to work with.

Not an agreeable person, perhaps?

Back when the 49ers were courting then-Stanford coach Jim Harbaugh, they made Baalke the general manager and this, as was reported early in the process, was an issue for Harbaugh. Early in Harbaugh’s rather successful tenure as head coach of the team, there were reports that he didn’t get along with Baalke and that their relationship was “strained.” Harbaugh finished his NFL head coaching career with a 49-22-1 record.

When Harbaugh was eventually fired — er, “mutually parted ways” with the team — there was more talk that Baalke was hard to deal with. Harbaugh, who took the 49ers to three consecutive NFC Championship games and the Super Bowl, rubbed Baalke and York the wrong way.

Enter Tomsula, the former defensive line coach who was seen as a yes man who would listen to Baalke and York. This came after a failed courting of Adam Gase, a high-profile candidate who was reportedly offered the job. Baalke then turned around and withdrew the offer, adding in the requirement that Tomsula would have to be Gase’s coordinator. Gase didn’t want that and wasn’t happy with the way Baalke handled things.

Gase is now the head coach of the Miami Dolphins, who have shaken off a slow start and won five games in a row.

And now there have been reports that Kelly and Baalke don’t get along and disagree on key issues, including what’s to be done at quarterback, where Blaine Gabbert has been benched in favor of Colin Kaepernick, who is playing at a decent-but-uninspiring level. There has been talk that failed first-rounder Christian Ponder could even be the starter next season.

Also, he’s not great at drafting

When Baalke won executive of the year in 2011, it was overlooked that Scot McCloughan — the former general manager who is currently having some success as Washington’s GM — actually built most of the thriving portions of San Francisco’s roster.

That year’s draft class included Aldon Smith (suspended several times, released), Kaepernick (benched for Gabbert, currently trying to earn a job next year), Chris Culliver (suspensions, left in free agency) and Bruce Miller (suspensions, released).

In 2012, Baalke had a draft class that includes just a single player still in the NFL. First-round wide receiver A.J. Jenkins never caught a pass in the regular season for the 49ers. Second-round pick LaMichael James was also a fairly high-profile bust.

In 2013, the 49ers did land two solid contributors, Quinton Dial and Eric Reid. Yet they also picked up players who struggled to find their way onto the field, like Tank Carradine, Vance McDonald, and Quinton Patton, not to mention the other six players who aren’t on the roster anymore.

High draft picks Chris Borland, Brandon Thomas, and Marcus Martin — all third-round picks — either retired (Borland), never saw action (Thomas), or were just terrible (Martin).

The jury is still out on 2015 and 2016, though several rookies failed to make the roster and injuries continued to be a theme for both draft classes.

WHY WITH THE ACLs EVEN?!

From 2013-14, Baalke used five of 23 draft picks on players coming off significant knee injuries. He spent picks in the second, third, fourth, fifth, and seventh rounds on these players. Marcus Lattimore and Trey Millard are both out of the NFL, while Carradine and Thomas, along with cornerback Keith Reaser, played an average of 103 snaps all season.

Last year, the 49ers spent a fourth-round pick on wide receiver DeAndre Smelter, who still is not healthy and probably will never play for the 49ers. This year, Baalke used a third-round pick on Will Redmond. He was six months removed from tearing his ACL at the time, and was placed on injured reserve by the 49ers.

Baalke loves injured players, despite the “redshirt” strategy not paying off to date.

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Early in his career, going up and getting the guys he wanted in the draft was seen as a big plus for Baalke. Now it just seems like the picks are getting worse and worse, though there is some potential for Arik Armstead and DeForest Buckner, first-round defensive ends taken over the past two seasons, to grow into a destructive force up front.

But they would be the exception rather than the rule at this point.

So firing Kelly isn’t a fix by any stretch. There is no doubt this season has been wretched for the 49ers, and Kelly had a short, ill-fated tenure as head coach of the Philadelphia Eagles. Many think he is better suited for the college game.

But what purpose would it serve firing a coach after just one season two years in a row? They would be approaching Cleveland Browns territory at that rate. Couple that with the fact that York himself said that the new 49ers coach would be expected to take the team to the Super Bowl in his first year (yeah, that ain’t happening), and it seems likely the 49ers are headed toward more instability that no coach would be able to handle.

Instead, the first place the 49ers should start handing out pink slips is their front office.