C. briggsae
Caenorhabditis briggsae
 Photo courtesy of (Eric Haag, All Rights Reserved.)

The Caenorhabditis briggsae genome assembly is based on sequence version cb25.agp8 deposited into WormBase as of 11 July 2002.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST, or a gene identifier, chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the C. briggsae genome. See the User's Guide for more information.

Request:
    Genome Browser Response:

chrUn Displays all of chromosome Un (only valid chr entry for this genome)
chrUn:1-1000000 Displays the first million bases of chrUn
R02870 Displays region of EST associated with GenBank accession R02870
U48289 Displays the region associated with the mRNA accession U48289
protein phosphatase PP2C Lists only records pertaining to protein phophatase PP2C
Kimble,J. Lists mRNAs deposited by co-author J. Kimble

Use this last format for author queries. Although GenBank requires the search format Kimble J, internally it uses the format Kimble,J..

Assembly details

This version was assembled from 2.05 million whole genome shotgun (WGS) reads, of which 88.2% were in read pairs. The Phusion assembler was used to assemble the WGS reads into contigs based on overlap information, and then into supercontigs using read pair information to cross gaps. These supercontigs were assembled into mapped ultracontigs based on FPC fingerprint mapping, with material from previously finished clones used to bridge gaps. Draft chromosome sequences are not available for C. briggsae, due to the lack of dense chromosomal maps that allow assignment of the ultracontigs to chromosomal locations. As a result, all data in this browser map to chrUn.

The N50 contig size in this assembly is 41 kb and the N50 supercontig size is 1450 kb. Most genes should be complete. The sequencing centers estimate that this whole genome shotgun assembly achieved 98% coverage of the genome.

The cb1 sequence and annotation data may be downloaded from the UCSC Genome Browser FTP server or Downloads web page. The sequence data have specific conditions for use. The cb1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: low-coverage.