Rear tire not centered?

It’s likely your wheel is not dished properly. I like to dish the wheel while it is in the frame to account for the fact that frames are not perfect down to 0.1mm. Most wheels are dished in a wheel stand.

Does it wobble when you spin it? Is there play in the hub?

AEyogi said:

Does it wobble when you spin it? Is there play in the hub?

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No it does not wobble. It's straight. No play too, though it developed slight play after a few rides, I removed the wheel and checked the where teh wobble is coming from. It was from the end cap, the bearings seem to be tight. I tightened the maxle and it seems to have solved it.

My vote is on the dishing.

Every MTB I've had is like that (though not a big sample size). The more important question though is where is the centerline of the wheel is in relation to the seat tube. Swingarms and chainstays can be asymmetrical and make it look as though the wheel is not centered. As long as the wheel is inline with the frame (seat tube as reference point) then there shouldn't be any tracking issues. Even if it was off by a few mm I bet you'd be hard pressed to notice in regular trail riding. You'd notice more when you tried to wheelie or manual and the bike kept trying to lean to one side.