We demonstrate high fidelity single-qubit gate operation in a trapped single neutral atom. The atom is trapped in the recently invented magic-intensity optical dipole trap (MI-ODT) with more stable magnetic field. The MI-ODT efficiently mitigates the detrimental effects of light shifts thus sufficiently improves the performance of single qubit-gates. The gates are driven with microwave, and the fidelity of gate operation is characterized by using the randomized benchmarking method. We obtain an average error per Clifford gate of $3.0(7)times10^{-5}$ which is much below the error threshold ($10^{-4}$) for fault-tolerance. This error is found to be dominated by qubit dephasing, and the corresponding coherence time relevant to the Clifford gates is also measured experimentally. This work is an essential step toward the construction of a scalable quantum computer with neutral atoms trapped in an MI-ODT array.
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