Fig. 3

Hypothetical mechanism of artifact SNVs and indels derived from enzyme-treated libraries. A Using Integrative Genomic Viewer, we observed that most of the unexpected, low VAF variants located in the reads contained soft-clipped regions. After further inspection of the sequence of a representative example read with a soft-clipped region, we found that the soft-clipped region consisted of the sequences originating from the strand opposite of its original alignment (blue arrow). The sequences were located at nearly perfect palindromic sequences (PS), which were naturally located at the reference genome (Red boxes). B A hypothesized mechanism of generating the example reads. Enzymatic activity exposes the PSs to generate the sticky end, enabling intra-molecular binding to produce a new chimeric template. C A hypothesized mechanism of the artifactual SNVs and indels induced by enzymatic fragmentation