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Figure 4 | BMC Genomics

Figure 4

From: Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

Figure 4

The allele frequency of GWAS SNPs. (A) The density distribution of allele frequency of GWAS SNPs among world populations. The distribution of GWAS SNPs in Turkey (TUR) is more similar to that of the European population (EUR) as compared to East Asian (ASN) and African (AFR) populations, indicating a greater proportion of ancestry sharing between TUR and EUR. Meanwhile, there is a higher proportion of common SNPs in both TUR and EUR than ASN and AFR, which is likely due to ascertainment bias in the GWAS studies as described in [35]. (B) The allele frequency of GWAS SNPs between Turkish (y-axis) and European (x-axis) populations. The red dots indicate SNPs in the 0.1 percentile (>0.345 allele frequency difference) of the absolute allele frequency distributions between Turkish and European populations. rs1129038 and rs12913832, both affecting HERC2 gene, are in strong linkage disequilibrium and, as such, have identical allele frequencies in European and Turkish populations. They are represented as two overlapping dots with 0.31 allele frequency in Turkish population (y-axis) and 0.71 allele frequencies in European population (x-axis). (C) The frequency distribution of derived and ancestral alleles for rs6712932 in Africa (ASW, LWK, YRI) Europe (CEU, FIN, GBR, IBS, TSI), Asia (CHB, CHS, JPT) and Americas (CLM, MXL, PUR) and Turkey (TUR). Note the increased frequency of the derived allele in the Turkish population.

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