Fig. 2

Hypothetical mechanism of artifact SNVs and indels derived from sonication-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 sequences originating from the strand opposite of its original alignment (blue arrow). The sequences were located at nearly perfect inverted repeat sequences (IVSs), which were naturally located in the reference genome (red boxes). B A hypothesized mechanism of generating the example reads. After fragmentation, a new chimeric template is generated through the intra-molecular binding of sticky ends of the IVS and the repair process. C A simulation mechanism of the hypothesis of the artifactual SNVs and indels induced by sonication fragmentation