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We experimentally observed state-independent violations of Kochen-Specker inequalities for the simplest indivisible quantum system manifesting quantum contextuality, a three-level (qutrit) system. We performed the experiment with a single trapped ^{171}Yb^{+} ion, by mapping three ground states of the ^{171}Yb^{+} ion to a qutrit system and carrying out quantum operatations by applying microwaves resonant to the qutrit transition frequencies. Our results are free from the detection loophole and cannot be explained by the non-contextual hidden variable models.

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