Supplementary Figure 1: Technical quality control metrics of targeted sequencing.
From: Loss-of-function mutations in SLC30A8 protect against type 2 diabetes
We computed various metrics to evaluate the quality of the initial sequencing experiment. Shown from the left are the distributions (over all sequenced samples) of the number of variant sites with 10x sequence coverage and hence nonmissing genotypes (Call Rate), the number of minor alleles in genotypes called across all variant sites (Minor Alleles), the number of minor alleles at sites where no other samples have minor alleles (Singletons), the fraction of genotypes called heterozygous (Heterozygosity), the ratio of the number of heterozygous sites to the number of minor allele homozygous sites (Het to Hom ratio), the fraction of sequence reads with the minor allele (averaged over all heterozygous sites; Allele Balance) and the fraction of minor allele genotypes identical to those called from Exome Chip or Metabochip genotyping (Concordance). Absent differential technical artifacts or population structure, distributions are expected to be similar between cases and controls. Statistical comparison between case and control distributions was performed via a Kruskal-Wallis one-way analysis of variance test.
