The standard capability of engine experimental studies is that ensemble averaged quantities like in-cylinder pressure and emissions are reported and the cycle to cycle variation (CCV) of indicated mean effective pressure (IMEP) is captured from many consecutive combustion cycles for each test condition. However, obtaining 3D spatial distribution of all the relevant quantities from such experiments is a challenging task. Computational Fluid Dynamics (CFD) simulations of engine flow and combustion can be used effectively to visualize such 3D spatial distributions. A dual fuel engine is considered in the current study, with port injected natural gas (NG) and direct injected diesel pilot for ignition. Multiple 3D CFD simulations are performed in series like in the experiments to investigate the potential of high fidelity RANS simulations coupled with detailed chemistry, to accurately predict the CCV. Measured valve lift profiles are used to specify the valve movements in the simulations. Cycle to cycle variation (CCV) is expected to be due to variability in operating and boundary conditions, in-cylinder stratification of diesel and natural gas fuels, variation in in-cylinder turbulence levels and velocity flow-fields. In previous publication by the authors (SAE 2016-01-0798), variability in operating and boundary conditions are incorporated into several closed cycle simulations performed in parallel. Stochastic variations/stratifications of fuel-air mixture, turbulence levels, temperature and internal combustion residuals cannot be considered in such closed cycle simulations. In the contrary, open cycle simulations with port injection of natural gas accounts for the stratifications, which in turn would give rise to CCV. This is the subject of the current paper. All the mean operating and boundary conditions are specified based on experimental conditions and author experience. The paper will try to isolate and quantify the effects of flow variable stratification on CCV.