Resolution:
## Figure 11.
Agglomerative haplotype analysis: testing for differences between two population samples'
homozygous segment length distributions. We compared the homozygous segment length distributions between JPT and CHB at each
locus position in the chromosome 20 masked ISLM_{cm }matrix by calculating the Cramer-von Mises two-sample minimum distance statistic ω^{2}. A representative position (Chr 20:43.82 Mb) with a high ω^{2 }value was chosen to illustrate the AHA permutation testing procedure. (a) ω^{2 }values between JPT and CHB for chromosome 20. (b) Segment length ECDFs for JPT and CHB at example peak ω^{2 }position. (c) Determination of significance level using permutation test: ECDFs from 100,000 resamples
after mixing JPT and CHB data and randomly reassigning group labels. ω^{2 }was calculated for each permutation resample, and the achieved significance level
calculated as the number of permutations with ω^{2 }values greater than or equal to the original two-sample ω^{2 }divided by the total number of permutations.
Johnson |