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PubMed Central, Figure 3: Nat Genet. 2016 Apr; 48(4): 359–366. Published online 2016 Feb 22. doi:  10.1038/ng.3510
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Nat Genet. Author manuscript; available in PMC 2016 Aug 22.
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Nat Genet. 2016 Apr; 48(4): 359–366.
Published online 2016 Feb 22. doi:  10.1038/ng.3510

Figure 3

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SNP haplotypes and sequence differences between HP subtypes inform structural history

(a) This alignment shows base pair differences between HP structural forms analyzed from 27 haplotypes. Only the polymorphic bases are depicted. The HP2FS haplotype contains a 300-bp segment with derived paralogous gene conversion from HPR (lavender) and a 250-bp region that is highly diverged between subtypes (green/pink). Each allele of the highly diverged region contains a mix of ancestral and derived alleles. The dashes reflect a 2-bp and a 7-bp indel; the other sites shown are individual SNPs. The sequence data used to create this alignment are available online (GenBank: KT923758-KT923784). (b) The frequency of each HP haplotype in four populations. (c) The earlier model of HP structural evolution (interchromosomal non-homologous recombination) would predict the HP1F SNP haplotype background (haplotype B) upstream of HP2 and the HP1S SNP haplotype (haplotype A) downstream of HP2. Additionally, it would predict Form R of the highly diverged region in HP2-Left. However, neither of these predictions was observed in any of the HP2 alleles in this study. (d) Both HP1F and HP1S can be created through simple deletions in HP2FS. The dashed lines indicate deleted sequence, while the dashed boxes indicate the sequence required to create each HP1 haplotype. The deletion model is also consistent with the observed SNP haplotype backgrounds surrounding the CNV.

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