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Watching James Paxton slowly negotiate the dugout stairs on the way to the clubhouse after three innings was a snapshot of the Yankees’ season.

High-end talent exiting a game with a physical problem has become commonplace for the Yankees, who had 13 players on the injured list when Paxton’s first pitch was delivered against the bumbling Twins at Yankee Stadium on Friday night.

Three innings, an unearned run and 64 pitches made up Paxton’s evening, and his exit came 4¹/₂ hours after Aaron Boone painted a positive picture about the injury front.

Then Paxton was finished and a faced a date with the Carl Pavano Memorial MRI tube to see how serious his cranky left knee is.

The fact Gary Sanchez hit two homers and the bullpen gave up two runs in six innings to steer the Yankees to a 6-3 win over the Twins in front of 35,911 took some of the sting out of losing Paxton.

Still, different variations of “hope’’ spilled out of mouths belonging to Boone, Brett Gardner and Paxton.

“Hopeful it’s just the soreness he has been dealing with, tonight on a damp night it was a little more cranky,’’ said Boone, whose club beat a team with a winning record for the first time this year and is 18-13.

“We are going to get it checked out, hopefully it is something quick,’’ said Paxton, who has been dealing with discomfort on the inside of the knee for most of the season but had it increase when he made the turn.

At the end of spring training Gardner said this club had more depth than any other team he was on. Like Boone and Paxton, the longest-tenured Yankee had his hope beads out.

“Hopefully it’s nothing too serious,’’ Gardner said of the 30-year-old Paxton, who has made seven trips to the IL since 2014. “He is a guy who wants the ball and go eight or nine. For him to come out he knows if he stayed out there he might have made it worse.’’

Before Paxton left the Yankees were getting healthier, with Miguel Andujar slated to come off the IL on Saturday and Aaron Hicks starting a minor league rehab Monday.

Because of a soft schedule and some timely performances from Gio Urshela and Domingo German, with help from Luke Voit, Sanchez, Gleyber Torres and DJ LeMahieu (who has missed the past three games), the Yankees not only have survived but thrived. Their .567 winning percentage at the start of Friday was third in the AL.

Considering how the Yankees have dealt with injuries this season, they have a chance of surviving anything the MRI exam uncovers in Paxton’s left knee that doesn’t require season-ending surgery, and a trade could fix that.

German was ticketed for the bullpen or Triple-A until Severino started the season on the IL and the thermometer-thin right-hander is 5-1 (tied for the AL lead in wins) and has a 2.56 ERA (seventh).

Urshela looks like Brooks Robinson at third and is no longer the out he was with the Indians and Blue Jays at the plate.

Tommy Kahnle, a mess last year when he worked more minor league games (26) to big league tilts (24), has filled the void Chad Green opened by not pitching well and then being demoted to Scranton/Wilkes-Barre. Kahnle fired a perfect seventh Friday night.

Yet, players such as Mike Tauchman, Mike Ford and Cameron Maybin have shelf lives. Ford’s expired when he was sent down after the game.

Instead of speculating what the MRI exam will discover or skip Paxton the next time around, Boone wasn’t getting ahead of himself.

“We will comment on it when we see something,’’ said Boone, who would love to see nothing.

That the Yankees’ injuries haven’t run them into a deep ditch is a testament to their depth.

Now the Yankees go through a ritual that has threatened to crush their season and hasn’t: news from the MRI tube.

“Hopefully we get decent news. He is a huge part of not only our rotation but our team,’’ said Gardner, using a word that has been tossed around far too often for the Yankees’ liking since spring training.

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