eGenome help: Interpreting maps

Interpreting maps

Note: Before attempting to view and interpret maps, it is strongly recommended that users first read the Chromoscape help sections.

Graphical views of chromosomal regions are displayed with the Chromoscape java application, which appears as a window separate from the user's browser. An example of a graphic is shown here and explained in detail below. This particular map is the result of a search for the region between D1S468 and D1S434, as outlined in the region search help page. For simplicity, not all elements within this region are shown here.

Chromoscape graphic example. Click on a feature for specific help about that feature.

By clicking on a feature in the graphic above, you will find information about that feature. For the main graphic display itself, the interpretation of the map is described in further detail below.

Graphic display

What is displayed. The default display will show only the region selected and the element types selected. In the example above, the defining markers D1S468 and D1S434 are both RH framework markers, so this region is displayed. If one or both of the defining markers are instead intervaled, the display will include all markers whose map positions are partially or completely overlapping with the positions of the defining markers. For example, if region-defining markers X and Y map to intervals B-C and D-E, respectively, then the region B-E encompassing all of this area will be displayed. If the display comes from an individual record or summary table (by clicking on the View Map or View Table buttons), the display includes one framework position above and below the region or element, such as intervals A-F for the preceding example.

All maps are displayed with orientation p terminus to q terminus from top to bottom. The sets of element types are displayed as tiers to the right of the RH framework, which is always shown at the left. Tiers are alternatively shaded white and gray, and the default order of the tiers is, from left to right: RH framework, RH markers, polymorphisms, bundles.

At left is the RH framework for the region selected, shown from D1S468 to D1S434 (45.7-105.5 cR) in the figure above. The vertical line represents the chromosome, and the positions of all markers are drawn in proportion to their actual centiRay positions. Reference distances in centiRays are shown to the right of the bar. The defined position of each framework marker is denoted by the thin line connecting the marker to the vertical line.

In the example, the RH framework is highlighted in red between markers D1S2731 and D1S450. This is to illustrate the region of the framework that the selected RH marker D1S508 maps within. The RH framework highlighting is a feature of Chromoscape which is discussed in detail here.

At right in the figure is shown the polymorphic tier, which consists of polymorphic markers intervaled relative to the RH framework. The first column, which starts with D1S468, has polymorphisms which map exclusively to an RH framework position. Notice that each of the 6 markers in this column are identical in name and position to the corresponding framework markers; this is not duplication of markers in the display but instead the placement of additional markers which have identical names but different primer sequences.

The remaining markers are all intervaled relative to the RH framework. For example, the highlighted marker D1S508 maps between RH framework markers D1S2731 and D1S450 with >1000:1 likelihood odds. The interval bar to the left of D1S508 depicts the range of the assigned interval. The other two markers in this group (D1S1612 and D1S160) also map to this interval. Note that the order of the markers D1S508, D1S1612, and D1S160 within the interval is unknown, and the order listed is not representative of their true order. Markers whose intervals touch or extend past the region displayed contain up or down arrows on the ends of their interval bars. Thus, D1S243's interval begins at D1S468 and continues up from there.

Selection of elements for further manipulation is performed by clicking once on the element name. Selection of an intervaled group is possible by clicking once on the corresponding interval bar. Clicking twice on a marker name opens a new browser window displaying the individual record for the marker. More information about selecting elements is here.