PMC

Sample depth of coverage. Histogram of the mean sequencing read depth per sample for 641 samples. 88% of the samples have mean depth less than 13, and 26% have depth less than 5.

Empirical kinship coefficents. Histograms of empirical kinship coefficients calculated from THUNDER genotypes. Each row contains all pairwise values that have the noted value for the pedigree-defined kinship coefficient. Thus, the lowest histogram ( φ_ped = 0.25) contains all full sibling and parent–child relations, the next row up contains grandparent-grandchild, avuncular, and half-sibling relations, and so on.

Concordance with exome chip. Concordance between exome chip genotypes and genotypes from three variant callers (a) and false positive rate (b). One point (at depth = 30.4, concordances between 96.7% and 98%) has been removed to expand the data region. The concordance is calculated only at the sites that are measured as non-monomorphic in the exome chip genotypes.

Frequency dependence of site finding. The fraction of variant sites found is dependent on both the frequency range of the variant, and the method used to call variants. The GATK Unified Genotyper in multisample mode finds more variants at all frequency ranges, but the disparity is most pronounced at the lowest frequencies, where the Unified Genotyper finds approximately 50% more variant sites than THUNDER. Single-sample Unified Genotyper calls follow a model that assumes a constant probability of finding any site in a single sample.

Allele frequencies in the NA Cohort. a). A two dimensional histogram comparing allele frequencies in the Native American cohort with those in European ancestry samples from 1000 genomes. The variants shown are the union of the two sets. Color scales logarithmically with the number of variants as in the colorbar above the image. b). One dimensional histogram of the difference in allele frequency for the same variants as shown in (a).