Photo courtesy of . Bill Branson, NHGRI
|
|
|
Cavia porcellus Photo courtesy of . Bill Branson, NHGRI |
The Feb. 2008 Cavia porcellus draft assembly (Broad Institute cavPor3) was produced by the Broad Institute at MIT and Harvard.
A genome position can be specified by the accession number of a sequenced genomic region, 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 guinea pig genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| scaffold_1 | Displays all of scaffold 1 | |
| scaffold_2:1-1000000 | Displays first million bases of scaffold 2 | |
| scaffold_123:1000000+2000 | Displays a region of scaffold 123 that spans 2000 bases, starting with position 1000000 | |
| chrM | Displays the mitochondial virtual chromosome | |
| | ||
| BX950328 | Displays a list of regions of mRNA with GenBank accession number BX950328 | |
| EB366004 | Displays region of EST with GenBank accession EB366004 on scaffold_1 | |
| | ||
| 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 | |
| Clerc,N. | Lists mRNAs deposited by co-author N. Clerc | |
| Use this last format for author queries. Although GenBank requires the search format Clerc N, internally it uses the format Clerc,N.. | ||
The guinea pig is one of 24 mammals whose genomes are being sequenced as part of the Mammalian Genome Project funded by the National Institutes of Health. While most of these genomes are slated for low-coverage (2X), a limited subset (including the guinea pig) are being sequenced to a higher quality of 6-7X.
This genome has been sequenced to 6.76X coverage with 95.55% of the bases assembled. The assembly totals 3143 scaffolds covering 2,722,377,657 bases (2.17% in gaps), with 50% of the scaffolds having a (N50) length of at least 27,408,292 bases (not including gaps). Approximately 97.52% of the contigs have been assembled into scaffolds of 200,000 bases or more. This genome assembly has a Q20 coverage of 5.99X with 99.57% q>=20 and 97.72% q>=50. The scaffolds have not been anchored to chromosomes in this assembly. However, the guinea pig mitochondrial sequence is available as the virtual chromosome chrM.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have specific conditions for use.
The guinea pig 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 this release.