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We study the possible impact of nuclear effects and final state interactions on the determination of the oscillation parameters due to mis-reconstruction of non-quasi-elastic events as quasi-elastic events at low energies. We analyze a disappearance experiment using a water \v{C}erenkov detector. We find that, if completely ignored in the fit, nuclear effects can induce a significant bias in the determination of atmospheric oscillation parameters, particularly for the atmospheric mixing angle. Even after inclusion of a near detector a bias in the determination of the atmospheric mixing angle comparable to the statistical error remains.

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