I've heard (and noticed) the rear wheel rub on the frame and front derailleur cage when pedaling standing up. The frame shows some paint wear at one spot. And, in the lowest gear, if I crank hard, I can hear the tire rub on the derailleur cage.

I'm riding a Kona Splice (20", 29er).

In the lowest gear, the front derailleur cage is pretty close to the tire as it is.

Should I upgrade parts? Tighten parts? Or not stand up at all knowing this?

Edit #1

Tires: Bontrager 29x2.1"

Edit #2

2013 specs show Geax Evolutions, 29x1.9"

Edit #3

Went lapping our backyard circuit just now. It would rub when climbing the east and west staights.

Pic of the rubbing on the frame (not as bad as I remembered):

Pic of me essentially pushing with my thumb, the tire fairly close to the frame:

However, if I try to move the rim, it doesn't move really. It would seem that it's only the tire/rubber? Under inflated perhaps? I'm around or below 30psi.

Edit #4

I actually have a 2012 model, confirmed with the color of the frame and the posted pics.

The specs show 29x2.1, and Vittoria Mezcal, why did the shop I bought the bike from swap those out for some Geax?

Also, why did the following models come with 29x1.9"? Also, in 2014, the Splice became a cross bike :/