People seem to be pretty worried about the Niners' run defense these days, and I've heard a lot of different explanations, usually attributed to individual players not performing well due to injuries or age, or whatever reason. Yes injuries have been a part, and probably some aging too. Maybe the change at FS had something to do with it. But I think there is a more important reason that people overlook: a conscious schematic decision by Fangio to sacrifice run defense for pass defense.

In 2011 nobody ran on the 49ers but we were a relatively mediocre pass defense. After the season, Fangio made a schematic adjustment and played much more nickel, even on base downs, putting only 6 men in the box and effectively daring people to run. Our rushing D has gotten a little bit worse but our passing D has gotten much better, and we've improved on 3rd downs. Overall this is a win for the Niner D, and it's hard to blame them for giving up a little more against the run given that the D-Line and LBs are being asked to stop the run with passing personnel .

Don't take my word for it, the numbers will bear this out.

By my rough calculations using PFF snap data for our nickel backs, here is how often we've played nickel the last 3 years:

2011 58.3 (601 out of 1030)

2012 65.2% (691 snaps out of 1060)

2013 64.5% (356 snaps out of 552)

This was easy for the Fangio years because he has maintained very stable substitution patterns. I looked at 2010 but it's a little harder to figure out the percentage of nickel packages from snap count stats because we played so many different combinations of DBs. Nonetheless, I am confident that the number is under 50%. We can be sure that Fangio took over a defense that was dominant against the run and leaky against the pass, and each year he has increased the use of passing personnel and decreased the use of the Nose tackle and run stopping personnel.

Here is how often other teams ran against us during that time:

2011 353 rushing attempts faced

2012 407 rushing attempts faced

2013 428 projected

So compared to 2011 we play nickel d on an average of 5-6 more snaps in every game, and at the same time teams are now attempting 3 to 5 more runs against us in each game.

So what was the result? On net, is this helping or hurting us in terms of stopping the other team? Here are the league rankings for the Niner D on some relevant stats:

Pass Yards YPA 3rd down % Rush Yards YPC 2011 16th 11th 11th 1st 1st 2012 2nd 2nd 4th 3rd 4th 2013 6th 7th 3rd 10th 10th

Against the pass we are much improved both in aggregate and on a per play basis, and we are also much improved on 3rd downs. I think in general in todays NFL it is more important to stop the pass than stop the run, and the evolution of the Niners personnel use on defense took place with that in mind. I'd like to think that this year's run defense will get better as we get Patrick Willis healthy and our mid-season reinforcements on the field, but the fact is that with the scheme we are running, we aren't going back to stoning every run at the line of scrimmage, and on balance, that's actually a good thing.

**Edit: Clarification - because of how I calculated these percentages from individual player's snap counts rather than from game charting, the number of dime package snaps are included in the nickel number. Basically wherever it says nickel in the article, you should read "sub-package". We don't play much dime at all, so the difference should be relatively minimal.

**Edit: Another factor came to light during the discussion, which is that in addition to playing more sub-packages, Fangio has progressively decreased the amount of snaps that he plays a safety in the box. This also seems to support the idea that he is making conscious strategic choices to strengthen pass defense at the expense of run defense.

Here are the approximate percentages of snaps with a safety lined up within 8 yards of the line of scrimmage:

2011:

Whitner – 39.2%

Goldson – 11.6%

Total snaps with a safety in the box (assuming no 0 coverage): 50.8%

2012:

Whitner – 32.2%

Goldson – 12.3%

Total – 44.5%

2013:

Hitner – 19.7%

Reid – 9.9%

Total – 29.6%