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The purpose of the
Assembly vs. STS Maps,
TPF vs. STS Maps, and
Merged Map vs. STS Maps 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-RH 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. For the TPF and Merged Map clone maps,
each clone is estimated to be 150Kb, and no overlap is assumed with adjacent maps.
Therefore, x-axis positions are only rough estimates and, in most cases, these estimates
result in chromosome lengths much larger than they actually are.
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 the corresponding Summary Page
(assembly,
TPF,
merged map)
with information about that particular contig.
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: Mon Dec 17 10:41:51 PST 2001
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