Figure 2

PLRD histograms by variant position and nucleotide change. Six example proband variants are shown with data from the proband (gold bar with star), as well as the proband's family and the background samples for the same variant change and position. The PLRD score is plotted versus the sample count. Blue bars indicate for that sample, that variant passed the GATK best practices variant filters. The samples with the red bars did not pass these same filters (wildtype/non-variant) and this variant was not called in their vcf file. The vertical black lines are marking the 3 (dashed line) and 6 (dotted line) standard deviation from the average PLRD score using only the assumed wild type/non-variant PLRD values (red bars, variant was not called). Bin numbers (as described in Methods) are given for each of the proband's variants shown. A) These two variant examples are called as Bin 1 and Bin 2 by the PLRD method and were Sanger verified as true variants. B) Examples of variants from all Bins that were only detected as wild type sequence by Sanger sequencing (false positive variants).