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In internal combustion engine computational fluid dynamics (CFD) simulations, uncertainties arise from various sources, such as estimates of model parameters, experimental boundary conditions, estimates of chemical kinetic rates, etc. These uncertainties propagate through the model and may result in discrepancies compared to experimental measurements. The relative importance of the various sources of uncertainty can be quantified by performing a sensitivity analysis. In this work, global sensitivity analysis (GSA) was applied to engine CFD simulations of a low-temperature combustion concept called gasoline compression ignition, to understand the influence of experimental measurement uncertainties from various sources on specific targets of interest-spray penetration, ignition timing, combustion phasing, combustion duration, and emissions. The sensitivity of these targets was evaluated with respect to imposed uncertainties in experimental boundary conditions and fuel properties.