Stereoscopic high definition video is one of the promising next-generation video services because 3D video can express more life-like visual experiences. 3D video quality of experience is affected by the employed codec and video format. Therefore, we conducted extensive subjective assessments for side-by-side and frame-sequential video sequences using different codecs. In this paper, we first show that the quality and depth perception of the frame-sequential video sequence are higher than those of the side-by-side video sequence for uncompressed video sequences. Then, using the encoded video sequences, we show that the quality and depth perception depend on the amount of spatio-temporal information and that a high-quality 3D video sequence with a MOS-Q (mean opinion score for quality with a five-grade scales) > 3.5, is required to achieve better depth perception than 2D video. Finally, we show that the naturalness of the encoded 3D video sequences correlates highly with the quality.