Bill Kostroun/AP file photoThe Niners’ defense

Bill Kostroun/AP file photoThe Niners’ defense

Despite personnel changes, defense leads way for 49ers

Only Vic Fangio and his defensive coaches saved the 49ers from another dreadful offensive day as they barely squeaked by the New York Giants on Sunday.

In the last two weeks, the Niners have barely beaten two teams that are now a combined 7-13. That’s not a team headed for the Super Bowl. More like one that won’t even make the playoffs.

Fangio continually comes up with schemes that frustrate opposing quarterbacks. Against the Giants, those schemes were the primary reason Eli Manning threw five interceptions, including one that realistically ended any chances of the Giants winning.

It isn’t just the schemes, either. The defensive coaches do a great job of coaching the players they have. This was supposed to be a down year for the defense, which suffered free-agent losses as well as an injury to NaVorro Bowman that has sidelined him all season. To make the situation even more serious, Patrick Willis has a toe injury that will require season-ending surgery.

No matter. Chris Borland has replaced Willis and played spectacularly well. A third-round draft pick, Borland has an excellent sense of where the play is going and he gets there quickly. He had two of the interceptions against the Giants.

Aaron Lynch is another pleasant surprise, and perhaps it’s time to salute general manager Trent Baalke for his draft-day surprises. Lynch is just a fifth-round pick, but he has played well enough to stay in the lineup as Ahmad Brooks went to the bench Sunday. Lynch had his third sack of the season and another two hits on the quarterback.

There’s another pleasant defensive surprise, cornerback Chris Culliver, who has become a superb cover corner. Time after time Sunday, he was playing very tight coverage, going up with receivers to knock the ball away without incurring a penalty, a very difficult assignment in this era when the rules strongly favor the offense.

If the offense were keeping pace with the defense, the Niners would be heading to the Super Bowl, but despite bringing in extra receivers to help the passing game, the offense is a mess.

As expected, the Niners ran well against the league’s worst run defense, with Frank Gore gaining 95 yards. Yet, even with the running game doing so well, the Niners got only one touchdown, on a great play by Michael Crabtree, who caught a medium-length pass and outran a defensive back for a 48-yard score.

The problem with the offense starts at quarterback. Colin Kaepernick can make spectacular plays, but there is no consistency to his game. He only had to call one timeout against the Giants because the play clock was running out, which is an improvement, but he has trouble handling snaps, whether under center or in the shotgun, he tripped up Gore on a handoff, causing Gore to fumble, he abandons pass plays too quickly to run. Occasionally, he still makes a good gain, but defenses are looking for that now, so more often than not, he is nailed for a loss.

Maybe he’ll learn, but I doubt it. That’s his gunslinger personality and it’s going to stop the Niners from getting back to the playoffs.

Glenn Dickey has been covering Bay Area sports since 1963 and also writes on www.GlennDickey.com. Email him at glenndickey36@gmail.com.

Chris BorlandGlenn DickeySan Francisco 49ersVic Fangio

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