Mitochondrial DNA D-loop. Imperfection around two high-variation segments (bp 1:800 and 16100:16350) of the D-loop of the mtDNA. Each position on the x-axis denotes the central nucleotide of the window examined. The y-axis shows the inferred imperfection by our direct method (solid grey line), imperfections inferred by the indirect method using fastPHASE (dotted black line), and the true imperfection (dashed black line), (a) bp 1 to 800. (b) bp 16100 to 16350.