Comparison of minor allele frequencies between AJ and CEU. a, Allele frequencies were computed for AJ first, and major and minor allele were assigned on the basis of which allele predominated. Therefore, no minor allele in AJ had a frequency greater than 0.50. Minor allele frequencies were plotted using the RcolorBrewer portion of the geneplotter library of Bioconductor in R. Default values were used for the smoothing. All 435,632 SNPs common to AJ and CEU were plotted. b, Karyogram highlighting markers with significantly different allele frequencies between AJ and CEU. Positions of significance are identified with black lines and centromeres are identified by gray. Lines drawn from the top indicate a higher minor allele frequency in AJ lines drawn from the bottom indicate a higher minor allele frequency in CEU. Counts on the right are the number of significant markers on the chromosome for AJ and CEU. The cutoff for significance is a Bonferroni-adjusted P-value of less than 0.05. Dense lines on chromosomes 2 and 6 are evidence for regions of gross allele frequency differences.
Olshen et al. BMC Genetics 2008 9:14 doi:10.1186/1471-2156-9-14