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PubMed Central, ED Figure 5.: Nature. 2015 Oct 1; 526(7571): 75–81. doi:  10.1038/nature15394
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Nature. Author manuscript; available in PMC 2016 Apr 1.
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Nature. 2015 Oct 1; 526(7571): 75–81.
doi:  10.1038/nature15394

ED Figure 5.

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(A) Deletion heterozygosity and homozygosity among human populations for a subset of high-confidence deletions. Populations from the African continental group (AFR) exhibit the highest levels of heterozygosity and thus diversity among humans, but show the overall lowest level of deletion homozygosity among all continental groups. By comparison, East Asian populations exhibited the lowest levels of deletion heterozygosity and the highest levels of homozygosity. (Het., heterozygous. Hom., homozygous.) (B) VAF distribution of major SV classes. Bi-allelic duplications represent a notable outlier, showing a striking depletion of common alleles, which can be explained by the preponderance of genomic sites of duplication to undergo recurrent rearrangement (see main text). As a consequence, most common duplications are classified as multi-allelic variants (i.e. mCNVs). (C) The number of base pairs (bp) differing among individuals within and between continental groups for deletions (upper panel) and SNPs (middle panel) contrasted with the ratio of deletion bp differences to SNP bp differences (deletion bp/SNP bp) among groups (lower panel). Non-African groups exhibit a higher deletion bp/SNP bp compared to Africans. (D) Neighbor-joining tree of populations constructed from MEIs (homoplasy-free markers) to provide a (simplified) view of population ancestry. The tree is labeled with the number of lineage-specific MEIs (Alu:L1:SVA). (E) Classification of ancestry in AFR/AMR and AMR admixed populations using homoplasy-free ancestry informative MEI markers. Color usage follows the same scheme as in Fig. 1d, except in the case of AFR individuals, which use both the color in Fig. 1d and another color that is unrelated to any other figure to indicate additional substructure within this group.

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