隨著科技的發展，DNA 定序的技術已進步許多。了解DNA 分子的核甘酸排列順序不僅能夠了解全基因組，同時能在醫藥、健康和其他領域有重大的突破。由於分子結構以及定序過程的不確定性，對鹼基定序的品質可能會有很大的影響。文獻已經廣泛探討過鹼基定序的品質，但是對鹼基位移的研究卻相當缺乏。現有研究雖已指出鹼基定序出現的位置並非固定，但對其位移的方向仍未得知。本研究利用轉移矩陣之方法，針對Illumina Miseq 平台的次世代基因定序資料監控鹼基的位移。研究結果顯示本方法確實能偵測週期之間鹼基的位移及位移的方向。

As science develops, the technology of DNA sequencing have progressed tremendously. Understanding the serial order of nucleotides within a DNA molecule will be a great help to realize the whole genome expression, and consequently make important breakthroughs in areas of medicine, health science and others simultaneously. Due to the variation of molecular structure, the accuracy of base calling does raise the issue of in the quality of sequence assembly. While the quality of base calling has been extensively investigated, the shift movement of bases is relatively unexplored. Several researches have been conducted and proved that the positions of bases are not fixed, however, the direction of shift movement has not been studied so far. The purpose of this thesis focuses on monitoring the shift movement of bases for next generation sequencing (NGS) data from Illumina Miseq platform by using transition matrix. The result of this study showed the existence of shifts over cycles, and the shift movement direction could be detected by the transition matrix method.

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