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In this paper, we propose a universal chroma subsampling strategy for compressing mosaic video sequences with arbitrary red-green-blue (RGB) color filter arrays (CFAs), which are widely used in the single sensor imaging pipeline, in H.264/AVC. We first develop a modified universal demosaicing scheme, which specifically recovers the G component in the color difference domain, to recover the missing color components in the input mosaic image frames. Then, based on the transform between the RGB and the YUV color spaces, the proposed universal subsampling strategy automatically samples, by considering the significance of the U and V components for reconstructing R and B pixels, the proper U and V chroma components according to the corresponding mosaic structure. To the best of our knowledge, this is the first universal chroma subsampling strategy designed specifically for mosaic video sequences with arbitrary RGB-CFAs. Experimental results on mosaic video sequences with seven common types of the RGB-CFAs demonstrate that the proposed universal chroma subsampling strategy is superior to the conventional strategy of H.264/AVC. Moreover, integrating the proposed universal demosaicing scheme and the chroma subsampling strategy can deliver better video sequence quality.