confidence score is a measure related to the distance between a given data point and the centroid of the nearest genotype cluster in a cluster plot. The heterozygosity of a sample is the fraction of non-missing genotype calls that are heterozygous. The genotype discordance rate is the number of genotype calls that differ between a pair of samples divided by the total number of SNPs for which both calls are non-missing. A Manhattan signal plot is a genome-wide plot of −log10 of the p-value for SNP-phenotype association versus chromosomal position. A regional association plot is a similar to the Manhattan plot except that it zooms in on a small region showing trait associations and will usually include SNP-SNP correlation data. Contrast QC (CQC) measures the separation of raw allelic intensities from Affymetrix arrays into three clusters. Genomic inflation factor [Devlin and Roeder 1999] is the ratio of the median of the observed statistic for a set of genome-wide tests to the expected median of that statistic under the null hypothesis. More details for some of these terms are given in Supporting Information.
