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Fig. 5 | BMC Bioinformatics

Fig. 5

From: Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect

Fig. 5

Empirical coverage of nominal 95% binomial prediction intervals plotted against the SNP’s minor allele frequency (MAF) in the original data. Prediction intervals are calculated for each SNP in each simulated data set using the SNP’s MAF in the original data as its true MAF. Empirical coverage for a SNP is calculated as the proportion of 1000 simulated data sets in which the SNP’s observed MAF was within its prediction interval. Each point represents empirical coverage for one of 10,279 SNPs in the simulations. The horizontal reference lines correspond to mean and median coverage across all SNPs (both 95% coverage, matching the nominal coverage) and to the 2.5th and 97.5th percentiles (93% and 97% coverage, respectively), One SNP at MAF = 0.051and with coverage less than 70% does not appear in the figure

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