While insertions were roughly twice as common as deletions in the Illumina runs, in general, indel error rates in both Illumina runs were two to three orders of magnitude lower than in the Roche/454 run. This is consistent with previous findings that mismatches are the predominant forms of error in Illumina, while indels are the most frequent errors in Roche/454 sequencing [20,22], showing that the GemSIM error-modeling approach captures these key characteristics of the different sequencing platforms.
