Monodelphis domestica Photo courtesy of Paul Samollow, Southwest Foundation for Biomedical Research, San Antonio. (NHGRI Press Photos)

The Oct. 2006 Monodelphis domestica draft assembly (NCBI project 12561, accession AAFR03000000) was produced by The Broad Institute.

### Sample position queries

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 Opossum genome. See the User's Guide for more information.

Request: |  | Genome Browser Response:
--- | --- | ---
chrX |  | Displays all of chromosome X
chr3:1-1000000 |  | Displays first million bases of chr 3
chr3:1000000+2000 |  | Displays a region of chr 3 that spans 2000 bases, starting with position 1000000
AF049753 |  | Displays region of mRNA with GenBank accession number AF049753
EC091556 |  | Displays region of EST with GenBank accession EC091556
CLOCK |  | Displays a list of genomic regions showing tBLASTn alignment of peptides from human CLOCK gene
NM_001033969 |  | Displays the region of genome with RefSeq identifier NM_001033969, the BCRA1 gene
immunoglobulin |  | Lists immunoglobulin regions
immunoglobulin light chain kappa |  | Lists only immunoglobulin light chain kappa mRNAs
miller |  | Lists mRNAs deposited by scientists named Miller
Miska,K.B. |  | Lists mRNAs deposited by co-author K.B. Miska

Use this last format for author queries. Although GenBank requires the search format Miska KB, internally it uses the format Miska,K.B.

### Assembly details

This draft of the opossum genome has approximately 6.8X coverage. The assembly length is nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, M (mitochondrial DNA), and Un (unmapped clone contigs). The N50 of the scaffolds including gaps is 60,456 kb; the N50 without gaps is 110 kb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The Broad Institute reports the following statistics for the monDom5 assembly:

- Total number of contigs in assembly: 72,811
- Total number of supercontigs in assembly: 5,344
- Placed contigs: 64,313
- Placed supercontigs: 216
- Unplaced contigs: 8,498
- Total bases in chromosomes 1 thru 8 and X: 3,502,373,038
- Total bases in chromosome Un: 103,241,611
- Number of gap bases (==N) in chromosomes 1 thru 8 and X: 89,779,610
- GC/AT ratio in chromosomes 1 thru 8 and X: 1,938,853,501/1,170,581,163 = 0.6037
- GC/AT ratio in chromosome Un: 50,094,290/38,955,502 = .7776

The monDom5 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. These data have specific conditions for use.

Many thanks to The Broad Institute for the opossum assembly data. The monDom5 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.