In the graphical display, the shade (in dense display mode)
or height (in full mode) of a vertical line indicates the score
of the best chained and netted alignment at that location.
Clicking on the track brings up detailed information about the
alignments in the currently displayed range of positions.
First, chains are derived from blastz and blat alignments as described in the description page of the Human Chain track. Subsequently, these chains were merged, sorted, and netted to obtain the best alignments. These methods are described in the Human Net track description.
The chaining and netting programs were developed at the University of California at Santa Cruz by Jim Kent. For more information, see Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D (2003). Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003.