We discuss the effects of non-standard neutrino interactions on muon rates in high statistics atmospheric neutrino oscillation experiments like IceCube DeepCore. We concentrate on the mu-tau sector, which is presently the least constrained. It is shown that the magnitude of the effects depends strongly on the sign of the Epsilon_MuTau parameter describing this non-standard interactions. A simple analytic model is used to understand the parameter space where differences between the two signs are maximized. We discuss how this effect is partially degenerate with changing the neutrino mass hierarchy, as well as how this degeneracy could be lifted.
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