PGM data, with some evidence to suggest the HFI were asymmetrically distributed across reads in the forward versus reverse orientation (or vice versa) [3]. We investigated whether any of the HFIs in our data were asymmetrically distributed across the forward and reverse oriented reads aligning across that site (see Methods ). This test was only performed on the 200 bp kits as the 100 bp kits had insufficient coverage for evaluation. Significant indel-strand asymmetry was detected in 7.4% (897/12,107) of the testable putative indel sites across the 200 bp datasets ( Table 2 ), with some datasets having a substantially higher percentage of asymmetric indels than others (i.e. 314-S-b-200, 314-S-a-200M). As with the HFI superset, these strand-asymmetric HFIs have more sites in common between runs than expected for a random event (Figure S2c and S2d).
