Figure 2. Accuracy of non-reference allele frequency estimation at HapMap/58C intersection variants for the Pool of 50 after duplicate removal.

An analysis of the correlation between the non-reference allele frequency estimates from the sequencing based variant caller and the allele frequency calculated from the reference genotypes. The analysis includes the true positive variants called by the sequencing based variant caller for which there were missing genotypes in the reference genotypes. The correlation coefficient is the Pearson's correlation coefficient. The figure shows the analysis for: (A) PCR enrichment, (B) aHC enrichment and (C) sHC enrichment.