MAF by sample type compared with CEU HapMap. Panel A: Distributions and scatter plot of minor allele frequency (MAF) deviations from CEU HapMap reference by locus and sample type. Box plot represents overall deviation from the HapMap by sample type. Horizontal line represents median deviation, top and bottom box boundaries delineate the 25th and 75th percentiles (IQR) and whiskers extend to 1.5 times the IQR above and below the box. Panel B: MAF deviations by sample type, clustered by HapMap MAF categories. Box plots are constructed as in Panel A.