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Fig. 1 | BMC Genomics

Fig. 1

From: 1000 human genomes carry widespread signatures of GC biased gene conversion

Fig. 1

Characterization of haplotypes of frequent genetic variants and putative case of BGC event. a - arrangement of computationally processed chromosomal segments for analysis of haplotypes. Autosomes have been divided into 56,328 segments, each containing 50 high-frequency (MAF > 25%) genetic variants. b An example of common haplotypes inside the segment 23 of Chromosome 1. Haplotypes were constructed from 50 adjacent high-frequency (MAF > 25%) genetic variants and are represented by the strings of fifty 0 s and 1 s, where “0” means the presence of a reference allele, while “1” means an alternative allele in the haplotype. The haplotypes that occur ≥100 times in the 1092 individuals are defined as ‘common haplotypes’ and are listed in descending order of their occurrence. The exemplified segment 23 has three common haplotypes. Putative BGC events were searched only in individuals who have one common haplotype and another nearly identical rare haplotype, which has only one allele difference with the common haplotype at the “acceptor” site (marked with a blue square). In this example such conditions were found in individual NA20787 from the TSI population. In the two parental haplotypes of TSI_NA20787, the first (Parent 1) is a common haplotype, which occurs 216 times in the 1092 genomes. The other haplotype (Parent 2), despite being identical to the common haplotype at 49 polymorphic sites, is a rare haplotype which occurs only once in the 1092 individuals. This rare haplotype contains the Acceptor site (marked with a blue square), which represents a case of putative base pair conversion event at this location in one of the ancestors of this individual. The location of this acceptor site in the haplotype string, its reference and alternative alleles, and base change due to BGC event (purple arrow) is shown in the bottom of the figure. Detailed information about every segment and all putative BGC events are available from our web site

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