Human Genome Working Draft Chromosome Reports
Please refer to the description in the following section as to the contents of these reports. Reports are available for the following freezes:

  Chromosome Reports Description
In effort to allow the users of the human genome sequence and the UCSC Human Genome Browser to evaluate the quality of the human genome sequence, 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.

Prior to the April 10, 2003 sequence (build33), the sequence was assembled computationally based on clone maps created by sequencing centers. Now that the genome is essentially finished, sequencing centers provide the complete final sequence - no assembly is performed.

Below is first a bit of background on the previous process for creating the assembled sequence followed by a description of what is contained within these web pages

As sequencing efforts became focused on producing finished sequence and identifying clones to fill in remaining gaps, the responsibility for each chromosome was assigned to a particular sequencing center, as follows:

Sequencing CenterContactChromosomes
Baylor College of MedicineSteve Scherrer 3, 12
Genoscope National Sequencing CentreJean Weissenbach14
Dept. of Energy Joint Genome InstituteEddy Rubin5
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 NCBI's Human Genome Sequencing web site.

Each center has been 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.

For the August 2001 assembly, the framework map on which the UCSC assembly is based shifted from solely the Washington University accession map to a combination of the TPF maps and the WashU accession map. Just like how a snapshot of sequences currently deposited in GenBank ("a freeze") is taken when creating an assembly, a snapshot of the TPF maps for each chromosome is taken. Since the TPF maps are a minimal tiling path possibly containing unsequenced clones not in the GenBank freeze, they are combined with the the WashU accession map using a dynamic programming algorithm developed at Ensembl to produce the final framework clone map on which the assembly is based.

The December 2001 and April 2002 assemblies were created by NCBI using no clone maps. Starting with the December 2001, UCSC no longer created a separate assembly of the genome.

The June 2002 and November 2002 assemblies were created by NCBI using TPF clones maps provided by the sequencing centers.

For each of 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 often be determined whether there is an error in one of the clone maps or a mistake in the conflicting information.

Feedback concerning both these webs pages and the underlying chromosome sequence on which they are based is encouraged. If there appears to be an error in a particular chromosome, 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.

For general comments regarding these web pages, please contact Terry Furey at UC Santa Cruz.

Terry Furey
Last modified: Tue Feb 26 14:01:09 PST 2002