In the present study, mixed-mode combustion of an E30 fuel in a direct-injection spark-ignition engine is numerically investigated at a fuel-lean operating condition using multidimensional computational fluid dynamics (CFD). A fuel surrogate matching Research Octane Number (RON) and Motor Octane Number (MON) of E30 is first developed using neural network based non-linear regression model. To enable efficient 3D engine simulations, a 164-species skeletal reaction mechanism incorporating NOx chemistry is reduced from a detailed chemical kinetic model. A hybrid approach that incorporates the G-equation model for tracking turbulent flame front, and the multi-zone well-stirred reactor model for predicting auto-ignition in the end gas, is employed to account for turbulent combustion interactions in the engine cylinder. Predicted in-cylinder pressure and heat release rate traces agree well with experimental measurements. The proposed modelling approach also captures moderated cyclic variability. Two different types of combustion cycles, corresponding to purely deflagrative and mixed-mode combustion, are observed. In contrast to the purely deflagrative cycles, mixed-mode combustion cycles feature early flame propagation followed by end-gas auto-ignition, leading to two distinctive peaks in heat release rate traces. The positive correlation between mixed-mode combustion cycles and early flame propagation is well captured by simulations. With the validated numerical setup, effects of NOx chemistry on mixed-mode combustion predictions are investigated. NOx chemistry is found to promote auto-ignition through residual gas recirculation, while the deflagrative flame propagation phase remains largely unaffected. Local sensitivity analysis is then performed to understand effects of physical and chemical properties of the fuel, i.e., heat of evaporation (HoV) and laminar flame speed (SL). An increased HoV tends to suppress end-gas auto-ignition due to increased vaporization cooling, while the impact of HoV on flame propagation is insignificant. In contrast, an increased SL is found to significantly promote both flame propagation and auto-ignition. The promoting effect of SL on auto-ignition is not a direct chemical effect; it is rather caused by an advancement of the combustion phasing, which increases compression heating of the end gas.