One of the problems that cause a decrease in the performance of the ultra-high bit-patterned magnetic recording (BPMR) system is track misregistration (TMR). Since the gap between data tracks is extremely narrow, it easily affects keeping the reader in the desired position. Therefore, this paper proposes the track misregistration mitigation included the estimation and correction techniques on singlereader/two-track reading (SRTR) BPMR using only a readback signal. The TMR estimation technique uses the convolutional neural network (CNN) to estimate the TMR level by the histograms of the readback signal enabling minimization of the complexity of the CNN structure and amount of training time. The estimated TMR levels obtained from the proposed CNN-histogram-based method will then be utilized to detect the estimated recorded bit by the CNN-based data detector. The simulation shows that our proposed system provides better TMR prediction accuracy even though the system has to face higher media noise. Furthermore, the CNN-based data detectors perform superior to the partial response maximum likelihood (PRML) based data detector, especially in strong electronic noise situations and the severe imperfection of recording media.INDEX TERMS Bit-patterned magnetic recording (BPMR), convolutional neural network (CNN), supervised learning, track misregistration (TMR).