By Sam McPherson

With a 1-9 record in the first year of head coach Kyle Shanahan’s tenure with the San Francisco 49ers, it’s obvious that this is not where the organization thought it would be heading into Thanksgiving. However, there have been many positives on the field beyond what the win-loss mark tells the casual observer.

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For the most part, Shanahan has the team playing very hard each game, and there have been a handful of games decided by close margins that could have gone either way—including two losses in overtime on the road. The 49ers also may have acquired their quarterback of the future, although that remains to be seen in the coming weeks.

Here’s a look at how the 49ers are stacking up now that we’re more than halfway through the season as they enter their bye week.

QB Problems Persist

San Francisco ranks eighth in the league in yards per rushing attempt. Unfortunately, the offense has not been able to capitalize on that strength due to problems with the QB position and resulting play calling from the sideline. Brian Hoyer went 0-6 as the starter with a 74.1 QB rating before being released, and rookie C.J. Beathard has been worse with a 70.8 QB rating despite his 1-3 mark as the starting quarterback.

With that inconsistent air game, running back Carlos Hyde’s 592 yards on the ground haven’t meant as much. The 49ers have not been been able to sustain long drives with a 56.3 completion percentage from the QB position, and once defenses stack against the run and force S.F. to beat them through the air, it’s been hard for the 49ers to move the ball with regularity.

Hyde also leads the team with 42 receptions, which is indicative of just how many dumpoffs the QBs have been forced to make when they’re unable to throw downfield to a wide-receiving corps that has suffered injuries and tight coverage itself. The 49ers are 21st in the league when it comes to total yards, but the time of possession average is 31st in the NFL (27:20), and that has hurt the defense repeatedly in close games.

Defense Shows Potential

Yes, the team is 28th in yards allowed. However, the 49ers defense has played fairly well, all things considered. There have been personnel changes, injuries, and a lot of playing time on the field with the offense struggling so much. The fatigue factor has been huge, too, as the 49ers have struggled to get off the field on third downs and late in games.

Those factors considered, the S.F. defense is actually 20th overall in yards per play allowed, which is more revealing than the total yards (because of the number of plays the defense has faced). That’s a better measure of where this defense is headed. Injuries to top rookie picks—defensive lineman Solomon Thomas (26 tackles, two sacks in eight games) and linebacker Reuben Foster (32 tackles in four games)—haven’t helped, either.

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Once the team solidifies its health and the lineup becomes more firm with added talent, this defense will be a very good one. It is showing the promise right now; it just needs a bit more time and injury luck to get back to a place of being feared by opponents. An improved offense will help the defense, too, in terms of the numbers of plays it has to defend.

Room For Improvement On Special Teams

The punt-return team has been average (9.0 yards per return), while the punt-coverage squad has been stellar (2.5 ypr). The kick-return effort has been mediocre (18.5 ypr), and the kickoff coverage has been somewhat bad (25.1 ypr). There’s room for improvement there, of course.

At 44.8 yards per punt, though, Bradley Pinion is having the best season of his three-year NFL career, and he’s just 23 years old. Placekicker Robbie Gould has been good—missing just two field goals and one extra point—but the missed kicks have come at the wrong times and may have cost the 49ers a few wins.

Is Conservative Play Calling Holding The Team Back?

The conservative play calling on offense can be explained away somewhat by the limited abilities at the QB position and the injuries to the WRs, but Shanahan still has to demonstrate he’s an offensive mastermind whether the talent is there or not. It’s the NFL, and his offense’s problems have hurt the defense and cost the team wins. How many weeks in a row did the 49ers lose a game in the final minutes? Better coaching gets at least two more wins in that stretch.

Of course, the wins don’t matter right now as much as the roster management, and Shanahan has shown the ability to work with general manager John Lynch effectively enough to make improvements there. Plus, as noted, the 49ers are playing hard even though they’re losing. They won’t necessarily be an easy out in the final six games of the season, despite the 1-9 record.

Looking Ahead

The big question for the Nov. 26 game at Levi’s Stadium against the hated Seahawks will be at the QB position. Jimmy Garoppolo wasn’t acquired to sit on the bench, and if Shanahan and his staff really are the offensive gurus they’re proclaimed to be, then expect to see Garoppolo start the final six games of the season. Beathard still needs a lot of work, and he could be a good NFL QB by 2019. But for now, the future is Garoppollo for the 49ers.

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The bad news is that the schedule is very tough for San Francisco down the stretch, so the team may not win another game, anyway. After Seattle (6-3), the 49ers go to Chicago (3-6) and Houston (3-6) in consecutive weeks before returning home to face Tennessee (6-3) and Jacksonville (6-3). Finally, San Francisco closes the season with a trip to Los Angeles to face the division-leading Rams (7-2). It will be interesting to see how the team handles these final six games—and how far that goes to setting a tone for 2018.