We present a precise lattice QCD calculation of the contribution to the neutron-proton mass splitting arising from strong isospin breaking, $m_n-m_p|_{QCD}=2.32pm0.17$ MeV. We also determine $m_{Xi^-} - m_{Xi^0}|_{QCD} = 5.44pm0.31$ MeV. The calculation is performed at three values of the pion mass, with several values of the quark mass splitting and multiple lattice volumes, but only a single lattice spacing and an estimate of discretization errors. The calculations are performed on the anisotropic clover-Wilson ensembles generated by the Hadron Spectrum Collaboration. The omega-baryon mass is used to set the scale $a_t^{-1}=6111pm127$ MeV, while the kaon masses are used to determine the value of the light-quark mass spitting. The nucleon mass splitting is then determined as a function of the pion mass. We observe, for the first time, conclusive evidence for non-analytic light quark mass dependence in lattice QCD calculations of the baryon spectrum. When left as a free parameter, the fits prefer a nucleon axial coupling of $g_A=1.24(56)$. To highlight the presence of this chiral logarithm in the nucleon mass splitting, we also compute the isospin splitting in the cascade-baryon system which is less sensitive to chiral dynamics. Finally, we update the best lattice QCD determination of the CP-odd pion-nucleon coupling that would arise from a non-zero QCD theta-term, $bar{g}_0 / (sqrt{2}f_pi) = (14.7pm1.8pm1.4) cdot 10^{-3} bar{theta}$. The original lattice QCD correlation functions, analysis results and extrapolated quantities are packaged in HDF5 files made publicly available including a simple Python script to access the numerical results, construct effective mass plots along with our analysis results, and perform the extrapolations of various quantities determined in this work.
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