Extended Data Figure 9 : UK10K-cohorts, population fine structure in the TwinsUK sample.

From: The UK10K project identifies rare variants in health and disease

Extended Data Figure 9

a, Chunk length matrix for all UK10K defined geographic regions, calculated as described in the methods. The bottom 5 regions are merged in Box 1 Figure. b, Coancestry matrix for all UK10K defined geographic regions, calculated as described in the methods. c, Chunk length matrix for all UK10K FineSTRUCTURE inferred populations, calculated as described in the methods. d, Coancestry matrix for all UK10K FineSTRUCTURE inferred populations. Details on calculation of these parameters are described in Methods. e, Pairwise coincidence matrix for the UK10K FineSTRUCTURE MCMC run, showing the fraction of the 1,000 retained iterations from the posterior in which each pair of individuals is in the same population, averaged for each pair of populations. The full posterior is extremely complex, which is indicative of a continuous admixture cline rather than discrete populations. f, Sources distribution for the FineSTRUCTURE inferred populations with the full set of inferred populations and geographic labels. Geographic labels of London, Southeast, North Midland, Southern and Eastern are merged into South and East for Box 1 Figure. FSPop labels are given to populations inferred by FineSTRUCTURE, which are merged into the Pop labels as shown in the main Box 1 Figure. g, The f2 haplotype age analysis estimates the time to the most recent common ancestor (tMRCA) between the two haplotypes underlying a given observed variant of allele count 2 in all of the TwinsUK samples. The observed IBD segment length around each f2 variant estimates the tMRCA, using an explicit model parameterized by the recombination and the mutation rates. Shown is the map of the UK with all regions used in this analysis depicted by their location, and lines colour-coding the observed median tMRCA of f2 haplotypes.