| | | Users Guide for STS Maps vs. Genome Sequence Asembly Comparison Plots | 
 |  | |  | The purpose of the STS Maps vs. Genome Sequence Assembly
	scatter plots is to show the correspondence between previously
	constructed genome-wide STS maps and the different clones
	maps.  We show one plot for each chromosome that displays the
	STS marker posistions for the Genethon, Marshfield, GeneMap99,
	G3, TNG, Whitehead Integrated and Whitehead-YAC maps.  The
	y-axis of the plots represent positions in the STS maps, while
	the x-axis represents positions in the clone maps.  The
	primary plots are scaled to fit an entire chromosome on one
	page. Additional plots are available which show portions of
	each chromosome in fixed scale 50mb windows and 10mb
	windows.
      
        Each STS marker is represented by a point that is colored and
        shape-coded as described in the legend in the upper right
        corner. The horizontal position of the point is the location
        of the marker on the clone map of the chromosome in
        megabases. The vertical position of the point is the distance
        of the marker along the chromosome as determined by one of the
        seven STS maps. All seven maps are scaled to have comparable
        distance ranges to facilitate comparison. Some markers map to
        different chromosomes entirely. These are shown at the top of
        the display.
      
        As you mouse-over the graph, the contig you are in, as
        determined by your horizontal position, is displayed in the
        little window at the bottom of the browser. (Position of this
        is dependent on the browser and platform being used.) Clicking
        on a contig will bring up a corresponding Summary Page which
        is part of our 
        Chromosome Reports web pages.  This Summary Page displays
        information about that particular contig with links to more
        detailed information.
      Caveats: 
	Due to the resolution, it is hard to pinpoint the clone
	contig for some markers. Go to a higher resolution plot if it
	appears that the marker you clicked on is not included in the
	report you get.  
	We use BLAT to place STS markers, but do
	not require an exact match of the STS sequence and/or primer
	sequences.  This will cause some false positive placements,
	and some false negatives as well, mainly due to the draft
	nature of the sequence.  
        We have not yet incorporated LOD
	scores for the markers. 
	There are limitations of the
	accuracy of each of the seven maps, for more details see 
	"Initial
	sequencing and analysis of the human genome," by the
	International Human Genome Sequencing Consortium, Nature,
	409:860-921.
       Terry Furey
	
	
Last modified: Fri Mar 22 13:48:36 PST 2002
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