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