There has been increasing demand to develop effective computer-assisted language training (CAPT) systems, which can provide feedback on mispronunciations and facilitate second-language (L2) learners to improve their speaking proficiency through repeated practice. Due to the shortage of non-native speech for training the automatic speech recognition (ASR) module of a CAPT system, the corresponding mispronunciation detection performance is often affected by imperfect ASR. Recognizing this importance, we in this paper put forward a two-stage mispronunciation detection method. In the first stage, the speech uttered by an L2 learner is processed by an end-to-end ASR module to produce N-best phone sequence hypotheses. In the second stage, these hypotheses are fed into a pronunciation model which seeks to faithfully predict the phone sequence hypothesis that is most likely pronounced by the learner, so as to improve the performance of mispronunciation detection. Empirical experiments conducted a English benchmark dataset seem to confirm the utility of our method.