FIG 2.

Validation of integrations. Edited output of the BreakAlign program showing a few representative chimeric NGS reads that span the integration site of unfixed loci. In each read, part of the sequence is viral (red lowercase nucleotides) and the other part aligns to the reference preintegration sequence shown above (on a black background). For each locus, we have chimeric reads from upstream and downstream flanks of the integration, both of which contain the 5-nt-long or (unless indicated) 6-nt-long target site duplication (TSD). Loci found in TCGA patients that are not shown here are described by Marchi et al. (33).