The three-dimensional variational technique (3DVar) is a popular technique used for data assimilation. Background error covariance (BEC) influences the performance of 3DVar technique. In this study, two formulations of BEC, namely the cv5 and cv6 options in the 3DVar assimilation in the Weather Research and Forecasting (WRF) model, are compared. It is found that the formulation of BEC impacts the analysis. Utilising the cv6 option moderately improves the simulation of monsoon depressions.