Figure 2.

Genetic markers. (A) To display genetic markers on the chromosome of interest, start with the top-level ‘Keyword Search’ view by selecting species as ‘medaka-chr.’ (B) Specify the chromosome number by inputting “CH” followed by the number, e.g. ‘CH01’ or ‘CH16’. (C) Clicking the ‘Search’ button presents all genetic markers horizontally along the chromosome. The distance of a genetic marker from the head of the chromosome is shown in terms of centimorgan (cM). Ultracontigs (series of scaffolds) are categorized into three groups, mapped, unoriented and unordered. Mapped ultracontigs are anchored on the chromosome by multiple genetic markers among which at least one recombination is observed. Unoriented ultracontigs are associated to the specific position on the genetic map, but their directions are unknown because no recombination is observed in the ultracontigs. A cluster of ultracontigs is unordered if it is located on the genetic map but neither the order in the cluster nor the orientation is known because no recombination is observed in the cluster. (D) An enlarged view of the window bounded by two vertical, red lines in Figure 2C. The ultracontig illustrated in the figure has four scaffolds linked by horizontal black lines that represent BAC end pairs. The four blue lines connected to one of the scaffolds from the node labeled with 0.07 cM indicate genetic markers among which no recombination is observed. (E) Clicking the leftmost, blue genetic marker name presents the list of markers surrounding the selected marker. (F) Selecting the scaffold enclosed in the red box displays the view with a variety of precise information associated with the scaffold, which is similar to Figure 1.