Similar to Roche 454 pyrosequencing [11], [12], indel-error rates increase with distance from the read start ( Figure 3a ). We also find that the substitution error rate increases towards the 3′ end of the read ( Figure 3b ). Error rates were higher on the 316 chips, and the low G+C% organism (S. tokodaii) had a higher error rate than the mid G+C% organism (B. amyloliquefaciens) across all datasets. The high mean indel error rate in the 200 bp manual kit appears to be due to a more rapid deterioration in base calling accuracy along the length of the read relative to the 200 bp OneTouch kit ( Figure 3a ).
