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Fig. 1 | BMC Genomics

Fig. 1

From: Intricacies in arrangement of SNP haplotypes suggest “Great Admixture” that created modern humans

Fig. 1

Haplotype construction and characterization. a Example of two parental haplotypes from segment 12 on chromosome 4 of CEU_NA07357 individual from 1000 Genomes. Following the 1000 Genomes Project, “0” means the presence of a reference allele, while “1” means an alternative allele in the haplotype. Only frequent GVs (with minor allele frequency >25%) have been used to construct haplotypes. In the last “Ancestral” line, “R” means that the reference allele is ancestral, “M” means that alternative (mutant) allele is ancestral, and “X” means unknown ancestral/derived status for the GV in the 1000 Genomes dataset. Information about every GV (identifier, location, alleles) and every haplotype are available from the Additional file 1: SD1. b Chromosomes have been divided into segments of equal length (500 Kb). From the beginning of each segment, 50 adjacent high-frequency GVs have been selected for construction of the haplotypes. When less than 50 frequent GVs were present inside the segment, this segment was elongated until a full-length haplotype with 50 GVs was complete (see Seg 4). c All haplotypes within a segment from 1092 individuals were grouped and ranked by the number of occurrences. Haplotypes that had been counted 100 or more times were named as common haplotypes (CHs). On 1b three common haplotypes exist and are shown above the solid line

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