Figure 2.

A sequencing context breakdown of the empirical insertion error rate of the two platforms on NA12878 whole genome data. In this figure we show all contexts of size 8 that start with AAAAA. The empirical insertion quality score (y-axis) is PHRED scaled. Despite the higher error rate (approximately Q12) of the PacBio RS instrument, the error is independent of the sequencing context. Other platforms are known to have different error rates for different sequencing contexts. Illumina's HiSeq platform, shown here, has a lower error rate (approximately Q45 across eight independent runs), but contexts such as AAAAAAAA and AAAAACAG have extremely different error rates (Q30 versus Q55). This context-specific error rate creates bias that is not easily clarified by greater sequencing depth. Empirical insertion error rates were measured using the Genome Analysis Toolkit (GATK) - Base Quality Score Recalibration tool.