Fig. 3: LD structure of the mtDNA variants.
From: Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population
LD structure of the common mtDNA variants identified by WGS. a Distributions of the haplotype correlations (r2) and b distance-dependent LD decay in the mtDNA and nDNA variants are illustrated in parallel. LD calculation of the nDNA variant pairs was adjusted for the distance corresponding to the mtDNA length (±8.3 kbp, P = 0.21 [R = 0.022] and P = 1.0 × 10−7 [R = −0.092] for mtDNA and nDNA, respectively). Distance-dependent LD decay in nDNA is highlighted with red. c Distributions of the number of the tag variants (r2 ≥ 0.5) per a common variant. d Pairwise LD matrix among the common mtDNA variants (MAF ≥ 5%). In the upper panel, the r2-values are colored according to the legend. In the lower panel, the variants without any tag variants are highlighted in gray, whereas the variants included in the common haplotypes spanning the entire mtDNA are separately colored as in the legend. Mitochondrial gene positions in mtDNA are indicated in the legend.
