Figure 4

Distribution of variant fraction vs. coverage per base for SNPs called only in single exome sequencing runs, not replicated in any other exome run. For the six different exome sequencing runs, the majority of single-run called SNPs fall below the 0.20-0.25 variant fraction for reliable heterozygous calls; those single-run calls with higher variant fractions (>0.20) generally fall below the 10x coverage cutoff. The run that had the most 'private' calls was the PGM run; however the majority of these private calls fall within the low variant fraction portion of the distribution suggesting that most of them are false positives. Interestingly, the distribution of 'private' SNPs in the Proton exome sequencing run is more scattered and distributed in the coverage and variant fraction ranges usually observed for true positive variant calls.