Colin Kaepernick shows he should be Niners' No. 2 quarterback

1:17 AM ET

SAN DIEGO — On Tuesday afternoon, a reporter asked San Francisco 49ers coach Chip Kelly if Colin Kaepernick was one of the two best quarterbacks on the roster. Kelly quickly and simply responded yes.

On Thursday night at Qualcomm Stadium, Kaepernick added a little more clarity to that statement, playing well enough to show that he is one of the team’s two best quarterbacks but also that he’s clearly No. 2 behind Blaine Gabbert.

Kaepernick started the Niners’ 31-21 victory over the San Diego Chargers in the preseason finale and finished 11-of-18 for 103 yards with four carries for 38 yards. Working against San Diego’s defensive backups and with San Francisco’s second-team offense, it wasn’t the type of performance that should win Kaepernick the starting job, but it was enough to show that there is still a drop-off from Kaepernick to backups Jeff Driskel and Christian Ponder.

Kaepernick handled the added attention stemming from his decision not to stand for the national anthem, leading a touchdown drive on the game’s opening possession while boos rained down from Chargers fans. That should only add to the case that Kaepernick is still the Niners’ best option behind Gabbert. But if that wasn’t enough, rookie Driskel replaced Kaepernick in the third quarter and promptly threw interceptions on his first two attempts.

Kelly has repeatedly said that the decision on which quarterbacks the 49ers keep will be made for football reasons. If that’s the case and the 2017 financials don’t factor, Kaepernick should remain a 49er after this weekend’s cuts to the initial 53-man roster.

QB depth chart: Gabbert did not play against the Chargers, as Kelly predicted. Kaepernick got the start and played 32 snaps — the entire first half — before calling it a night. Driskel and veteran Ponder followed to close out the game. Ponder rallied the Niners with two late scoring drives, both capped by his rushing touchdowns.

Reid kneels, then sits: Kaepernick said Sunday he didn’t ask any of his teammates to join his silent protest because he knew the consequences and potential backlash that came with his stance. But safety Eric Reid apparently didn’t mind as he kneeled next to Kaepernick during the national anthem Thursday. When it was over, Reid and Kaepernick stood and embraced before Kaepernick led the offense onto the field for the opening drive. Reid was one of many expected starters who did not play.

Nate Boyer visits: Nate Boyer, the former U.S. Army Green Beret and Seattle Seahawks long-snapper, attended the game and stood on the sideline next to Kaepernick and Reid during the national anthem. Kaepernick invited Boyer after reading the note Boyer wrote to him on earlier this week. Boyer said he and Kaepernick discussed their respective stances on Kaepernick’s protest and talked about ways they could potentially work together moving forward.

Most starters sit: The list of presumptive 49ers starters who played is much shorter than the list of those who didn’t. None of the team’s expected defensive starters suited up and offensive lineman Zane Beadles was the only one on offense in uniform. If that wasn’t enough to show that Kelly and the Niners just wanted to get out of the game healthy, the long opening drive that featured 16 plays and the Niners huddling should have been.

A surprise player who impressed: Maybe it’s not a surprise at this point because he’s the 49ers’ preseason MVP, but linebacker Marcus Rush was at it again Thursday night. He had two sacks, including a forced fumble, and an interception to help San Francisco rally for the win. Rush finished the preseason with six sacks and is going to be awfully tough to leave off the 53-man roster come this weekend.

Up next: The 49ers can now officially turn their attention to the season opener against the Los Angeles Rams on Sept. 12. Before they do, they’ll have to make 22 roster moves to get to the league-mandated 53-man roster by Saturday at 4 p.m. ET.

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