Ensembl Pika

Example Data Points

This release of Ochotona princeps data is assembled into scaffolds, so there are no chromosomes available to browse.

A few example data points :

• Scaffold: scaffold_21244
• Gene: CRYAA_OCHPR

About the Pika genome

Assembly

This is the first release of the low-coverage 1.93X assembly of the American pika (Ochotona princeps). The genome sequencing and assembly is provided by the Broad Institute.

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for supercontigs is 53.58 kb and is 3.27 kb for contigs. The total number of bases in supercontigs is 3.43 Gb and in contigs is 1.92 Gb.

Annotation

Owing to the fragmentary nature of this preliminary assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures,in order to present complete genes. There are 5501 such gene scaffolds, with identifiers of the form "GeneScaffold_1".

• Details of the gene-scaffold construction and subsequent gene-build

What's New in Ensembl 49

Ochotona princeps News

• ncRNAs - new data and patches
  Two ncRNA sets have been added, for pika and mouse lemur, and the ncRNA descriptions in human have been patched.

General News

• Release schedule
  

  Ensembl release 50 will occur in July (rather than in April as originally scheduled).
  Read more...

• API changes - regulatory features
  Regulatory feature support has been moved from the core API to the functional genomics API. More information about using the new code...
• Removal of viral genes
  We have removed a total of about 1200 viral genes from the following species.
  Read more...
• Mart updates
  RGD and SGD Symbol+ID combinations have been introduced, similar to HGNC, MGI and ZFIN. The issue with subsets of homologs being returned has been resolved.

More news...

Statistics

How the statistics are calculated