Gallus gallus Photo courtesy of Bill Payne, Michigan State University (NHGRI Press Photos)

The May 2006 chicken (Gallus gallus) v2.1 draft assembly was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, MO, USA (WUSTL).

### Sample position queries

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

Request: |  | Genome Browser Response:
--- | --- | ---
chrZ |  | Displays all of chromosome Z
chr3:1-1000000 |  | Displays first million bases of chr 3
chr3:23000+4000 |  | Displays a region of chr 3 that spans 4000 bases, starting with position 23,000
BX950328 |  | Displays region of mRNA with GenBank accession number BX950328
BU335953 |  | Displays region of EST with GenBank accession BU335953 on chr Z
chr27_1.383 |  | Displays region of genome containing Genscan gene prediction chr27_1.383
CWNT-8C |  | Displays region of genome with gene symbol CWNT-8C
NM_204735 |  | Displays the region of genome with RefSeq identifier NM_204735
374180 |  | Displays the region of genome with Entrez Gene identifier 374180
pseudogene mRNA |  | Lists transcribed pseudogenes, but not cDNAs
homeobox caudal |  | Lists mRNAs for caudal homeobox genes
zinc finger |  | Lists many zinc finger mRNAs
kruppel zinc finger |  | Lists only kruppel-like zinc fingers
zhang |  | Lists mRNAs deposited by scientist named Zhang
Taguchi,T. |  | Lists mRNAs deposited by co-author T. Taguchi
Use this last format for author queries. Although GenBank requires the search format Taguchi T, internally it uses the format Taguchi,T..

### Assembly details

In this assembly, 198,000 additional reads covering all contig ends and regions of low quality have been added to the original assembly's 6.6X coverage. Approximately 95% of the sequence has been anchored to chromosomes, which include autosomes 1-24, 26-28, and 32, and sex chromosomes W and Z. (In contrast to mammals, the female chicken is heterogametic (ZW) and the male is homogametic (ZZ).) The remaining unanchored contigs that could be localized to a chromosome have been concatenated into the virtual chromosomes "chr*_random", separated by gaps of 10,000 bp. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn_random", separated by gaps of 100 bp to reduce the total size of chrUn_random. The chicken mitochondrial sequence is also available as the virtual chromosome "chrM".

This assembly has the following statistics.

- ultracontigs: N50 = 15.5 Mb (n=19); longest ultracontig = 80.3 Mb (chr3)
- supercontigs: N50 = 11.1 Mb (n=26); longest supercontig = 52 Mb (chr2)
- contigs: N50 = 45 kb (n=5863); longest contig = 625 kb

In this context, a contig is defined as a contiguous stretch of DNA, a supercontig is a set of ordered/oriented contigs linked by read-pairing data, and an ultracontig is an ordered/oriented list of supercontigs. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

Although centromere positions are indicated on this assembly, little is known of their exact sequence. The centromeres of 18 chromosomes were tentatively localized based on FISH hybridization using BAC clones, genetic markers flanking the centromeres in coordination with mapping gaps in the physical map, repetitive sequence content, and analysis of proximity to the constrictions of the mitotic metaphase chromosomes. For more information on the process used to create the chromosomal sequences and assign centromere locations, see the WUSTL Gallus gallus assembly release notes.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The chicken browser 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 the success of this release.