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Detection of  de novo , low-frequency mutations is essential for characterizing cancer genomes and heterogeneous cell populations. However, the screening capacity of current ultrasensitive NGS methods is inadequate owing to either low-efficiency read utilization or severe amplification bias. Here, we present o2n-seq, an ultrasensitive and high-efficiency NGS library preparation method for discovering  de novo , low-frequency mutations. O2n-seq reduces the error rate of NGS to 10 −5 –10 −8 . The efficiency of its data usage is about 10–30 times higher than that of barcode-based strategies. For detecting mutations with allele frequency (AF) 1% in 4.6 Mb-sized genome, the sensitivity and specificity of o2n-seq reach to 99% and 98.64%, respectively. For mutations with AF around 0.07% in  phix174 , o2n-seq detects all the mutations with 100% specificity. Moreover, we successfully apply o2n-seq to screen  de novo , low-frequency mutations in human tumours. O2n-seq will aid to characterize the landscape of somatic mutations in research and clinical settings.

Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq