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The purpose of the STS Maps Detail pages is to allow a
comparison between the ordering of STS markers on the draft
sequence and their corresponding positions on the genetic (assembly, TPF, merged
map), YAC (assembly, TPF, merged map),
and radiation hybridization (RH) (assembly, TPF, merged map) maps. Currently displayed are
the Genethon and Marshfield genetic maps, the Whitehead
Institute YAC map, and the GeneMap99 GB4, GeneMap99 G3, and
Whitehead RH maps.
Each of the STS markers are placed on the assembled draft
sequence and the individual accessioned clones which are
available for a particular GenBank freeze. Phase 0 sequences
in the freeze are not considered. For STS markers for which
the full sequence is available, placement is done using Jim
Kent's BLAT program. For markers without full sequences,
placement is also done using BLAT with a FASTA sequence
constructed using the known primer sequences for the
STS.
The placements of the STS Markers on the assembled draft
sequence can also be seen in the corresponding freeze version
of the UCSC
Human Genome Browser under the STS Markers track.
The STS Maps pages summarize the results of these placements
in tables with the following columns:
- Links - links to other pages with information for this accession -
Summary(S), Genetic(G), YAC(Y), RH(R), BAC End Pairs(B), Overlaps(O)
- Contig - name of contig
- Accession - GenBank accession for clone.
- Chr Start - base pair in chromosome where STS marker sequence starts, or
beginning of accession if no markers placed on that clone.
- Phs - phase of sequence in freeze.
- STS Marker - name of the STS marker in the corresponding STS map
- (map) Chr - chromosome the marker is placed on in the STS map
- (map) - position the marker is placed at in the STS map
- Plc - number of times this marker is placed on this clone map
- Other Accessions - a list of the other accessions used
in this clone map on which this STS marker is placed.
Clicking on one of these will display the contig containing
the corresponding accession. Not all accessions for a particular
freeze are used in any of the clone maps due to redundancy
- All Accessions - a list of all of the accessions in the Genebank freeze
that this marker is placed on.
Each accession found on a clone map is required to appear at
least once in the table, but may appear multiple times if more
than one STS marker is placed on it.
There are separate tables for each of the contigs in a
chromosome. Each line in the tables is colored in order to
help identify agreements and disagreements between the clone
map and the STS maps. To determine the colors, each contig is
assigned a non-overlapping range of positions on an STS map.
The ranges are required to be ascending, and the concatenation
of the ranges of all contigs span all the possible positions
in the STS map. Based on this alignment, rows in tables are
given the following colors with the following interpretations:
- White - no STS markers are placed on this accession.
- Blue - the position of the STS marker on the STS map falls within the
range of positions assigned to this contig
- Green - the position of the STS marker on the STS map is slightly
outside the range of positions assigned to this contig.
For genetic maps, this is up to 3cM,
for the YAC map, this is up to 3 YACs, and for the RH map this is up
to 10 cR. Green lines near the edges of contigs are,
in most cases, fine and are probably due to the inability
of the STS map to correctly order markers at that resolution.
- Pink - the position of the STS marker on the STS map
differs from the range assigned to this contig, but the
marker is placed on the same chromosome.
- Red - the STS map places this marker on a different chromosome.
- Yellow - this STS marker is not placed on an accession
in this contig, but its position on the STS map falls within
the range of positions assigned to this contig
This coloring is provided to help identify possible
problematic areas in the assembly, and to verify the accuracy
of others. Keep in mind that for each individual table, there
are multiple sources of error that may color a particular area
a misleading color such as -
- A marker being incorrectly placed on a clone
- An error in the STS map
- An error in assigning STS map positions to a contig
Therefore, information should be used from all of the tables together to
draw any conclusions.
The pages are designed so that you can view one contig at a
time, or all contigs for a single chromosome at once. A
header frame is provided on each page to allow for easier
navigation through the table, to provide a reference for the
meanings of the line colors, and to display the table column
names for convenience when viewing longer contigs.
Warning: Many of the pages contain very large tables
and may take a while to load, especially for the larger
chromosomes. Please be patient.
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