Figure 3 .
Example position where bases are identified as sequencing errors by GATK but not ReQON. Plot A shows an Integrative Genomics Viewer (IGV) visualization of chr10:75,531,679-75,531,712 for cell line replicate 1, highlighting a position where the reference sequence is T but all of the bases mapped to this position are a C. This position (chr10:75,531,700) is not listed as a known variant in dbSNP version 132. The bases at this position are removed from the training set by ReQON but are called as sequencing errors by GATK. Plot B shows box plots comparing the quality scores of the bases at this position after recalibration with GATK and ReQON. Overall, ReQON assigns higher quality scores to these non-reference bases than GATK.
Cabanski et al. BMC Bioinformatics 2012 13:221 doi:10.1186/1471-2105-13-221