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This paper presents a study of the video compression effect on source camera identification based on the Photo-Response Non-Uniformity (PRNU). Specifically, the reliability of different types of frames in a compressed video is first investigated, which shows quantitatively that I-frames are more reliable than P-frames for PRNU estimation. Motivated by this observation, a new mechanism for estimating the reference PRNU and two mechanisms for estimating the test-video PRNU are proposed to achieve higher accuracy with fewer frames used. Experiments are performed to validate the effectiveness of the proposed mechanisms.