Performance of variant calling at germline SNPs.

True Positive (TP): ≥1 non-reference allele called by Affymetrix array, ≥1 non-reference allele called by sequencing.True Negative (TN): 0 non-reference alleles called by Affymetrix array, 0 non-reference alleles called by sequencing.False Positive (FP): 0 non-reference alleles called by Affymetrix array, ≥1 non-reference allele called by sequencing.False Negative (FN): ≥1 non-reference allele called by Affymetrix array, ≥0 non-reference alleles called by sequencing.True Positive Rate (TPR): TP/(TP+FN) = sensitivity = power.False Positive Rate (FPR): FP/(FP+TN) = 1-specificity.False Negative Rate (FNR): FN/(TP+FN) = 1 - sensitivity = type II error.