基因檢測是透過將個體的序列資料比對到參考基因體以識別個人基因體中的單核苷酸多態性、插入、缺失及大片段重組之變異。當參考基因體與個人基因體差異較大時，其比對可能會不精準，而導致變異誤判。目前很少有研究在評估參考基因體與個人基因體差異所引起變異誤判的程度。為探討此議題，本研究採用GRCh38基因體當作參考基因體及CHM1作為個人基因體，我們將兩種全基因體做序列比對得到的變異定義為正確的變異。接著利用模擬軟體模擬CHM1的次世代定序資料並比對到參考序列中來偵測變異，偵測到的變異若與正確變異不同即定義為變異誤判。我們發現在全基因體唯一比對的區域中，偵測到的變異與正確變異幾乎相同，但仍然存在數百個變異誤判。在非唯一比對區域中則發現約有兩萬個變異與正確答案不一致。這些變異誤判是由兩種不同的機制(基因片段複製與局部演化偏移)所造成。我們也進一步探討這些變異誤判是否發生於基因之中，發現有近百個基因可能受到誤判的影響。這些結果有助於評估是否建立族群專屬基因體參考序列之必要性。

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