In this tutorial we will view a linkage group and the contigs associated with it.

First choose a linkage group.

This opens a window with 2 panes. The Composite Map from SoyBase is on the right while the left pane shows only those markers which are associated with a contig in the physical map. The sizes and ends of the contigs are based on the number of bands in the FPC fingerprints. Although only approximate, the relative sizes should be accurate. Contigs were positioned on the map by centering them on the associated genetic marker(s).

Moving the mouse over a BAC or marker highlights all related map objects. In this example putting the cursor on the contig WmContig584 highlights the markers on the genetic map that anchor it.

Markers on the physical map have been renamed to indicate their linkage group and the method used to associate them with a contig. Complete details on the nomenclature can be found here.

A1_o_Satt165_1overgo derived from the SSR marker Satt165 associated with BACs by hybridization (membranes contained BACs from both the GMW1 and GMW2 libraries)
A1_p_Satt449_1SSR marker associated with a BAC using the UMC 6D pools (only BACs from the GMW2 library)
A1_m_Satt364_1SSR marker associated with a BAC using the ISU BAC superpools (only BACs from the GMW1 library)
A1_r_pB172_1RFLP marker associated with a BAC by hybridization using the ISU BAC superpools (only BACs from the GMW1 library)

Clicking on any feature on the physical map brings up a contextual menu of actions that can be applied to that map object. These figures show examples of a contextual menu (left) and both the mouseover highlighting in yellow and the semi-persistent highlighting available from the popup menu (right).


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