Chromosome Reports - Nov 2002 Freeze
Please refer to the description in the following section as to the contents of these reports. Reports are available for:

  Chromosome Reports Description
In effort to allow the users of the draft assembly sequence produced by NCBI and the UCSC Human Genome Browser to evaluate the quality of the assembled human genome, we have created a series of web pages that show comparisons with existing genome-wide sequence tagged sites (STS) maps, BAC end sequence pair information, and calculated clone sequence overlaps. Using this resource, areas in the genome of special research interest can be examined to determine whether the sequence information is accurate and reliable before expensive and time-consuming experiments are undertaken. Below is first a bit of background on the current process for creating the assembled sequence followed by a description of what is contained within these web pages

As sequencing efforts are being concentrated on producing finished sequence and identifying clones to fill in current gaps, the responsibility for each chromosome has been assigned to a particular sequencing center and are as follows:

Sequencing CenterContactChromosomes
Baylor College of MedicineSteve Scherrer 3, 12
Genoscope National Sequencing CentreJean Weissenbach14
Dept. of Energy Joint Genome InstituteJoe Monforte5
Los Alamos National LaboratoryNorman Doggett16
RIKEN Human Genome Research GroupTodd Taylor 11, 21 (21 consortium)
Sanger CentreJane Rogers1, 6, 9, 10, 13, 20, 22, X
Stanford Human Genome CenterJane Grimwood19
Washington University Genome Sequencing CenterRick Wilson2, 4, 7, Y
Whitehead InstituteChad Nausbaum8, 15, 17, 18

More information about the sequencing effort can be found at Ensembl's Human Assemblies Genome Server and NCBI's Human Genome Sequencing web sites.

Each center is responsible for producing a minimal tiling path (TPF) map representing their current ordering of clones across the chromosomes for which they are responsible. These clones need not be sequenced, yet, and thus sequence for them may not be deposited into GenBank.

Beginning with the December 22nd freeze, UCSC has switched to using the NCBI assembly. The reports generated here, then, are based on NCBI's build30 assembly. This is built using the TPF clone maps as the main input source. UCSC will no longer produce an assembled sequence of their own.

For the draft assembly sequence, web pages have been created showing how each of these compare with other sources of information. Currently, the user can view the correspondence between these clones maps and sequence-tagged site STS maps in both a scatter plot and in a tabular format. The STS maps employed in this analysis include the Genethon and Marshfield genetic maps, the Whitehead Institute YAC map, and the NCBI GeneMap99 GB4 and G3, Whitehead Institute, and Stanford TNG radiation hybridization (RH) maps. In addition, there is BAC End Pairs and Clone Overlap information. A Summary Page is provided that shows a high-level view of all of this information for each chromosome. Multiple sources of information are used because each has errors. With this combination, it can be determined often whether there is an error in one of the clone maps, or it is a mistake in the conflicting information.

Feedback concerning both these webs pages and the underlying clone maps on which they are based is encouraged. If there appears to be an error in a TPF clone map, please alert the chromosome coordinator for the corresponding chromosome as listed in the table above. Please include supporting evidence showing why the current map is not accurate. NOTE: The TPF maps displayed here represent the version used for a particular assembly. These maps are constantly being updated by each of the sequencing centers as new information becomes available. For general comments regarding these web pages, please contact Terry Furey at UC Santa Cruz.


Terry Furey
Last modified: Fri Dec 20 09:41:44 PST 2002