Figure 2.

Polarization of the raw read coverage. The top two plots show the raw read coverage along the reference sequence of locus 332172 for F0 B. variegata (A) and F0 B. bombina (B). The B. variegata individual is homozygous for the reference state (R) at all sequence positions, whereas the B. bombina individual has a number of variants. Two homozygous (156 and 343) and two heterozygous (110 and 224) variant positions are highlighted. For these four, the matrix entries are listed below the plots. A polarized matrix, M_p, is computed from these read counts (see text, C), in which sequence states associated with B. variegata have positive entries and sequence states associated with B. bombina have negative entries. For each sample, raw read counts are then multiplied by M_p. Average positive entries and average negative entries result in a B. bombina score and a B. variegata score, respectively, and when plotted in a coordinate system (D), samples can be assigned to three clusters representing BbHOM, HET, and BvHOM. Note that the heterozygous variants (B) do not interfere with the clustering into three diplotypes.