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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 second Ensembl 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

A standard Ensembl projection build was carried out whereby genes from the new human gene set (from release 48) were projected onto the pika assembly. Owing to the fragmentary nature of the preliminary pika assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures in order to present complete genes. There are 5537 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 50

Ochotona princeps News

• Pika reprojection
  A new genebuild has been made on the existing Ochotona princeps assembly, using the new human gene set.
• Non-coding genes
  These have been updated for most species, including an miRNA update and HGNC names where possible.
• Multiple alignments
  

  The multiple alignments are being extended with new species and 2X genomes.
  Read more...

• Blastz-net alignments
  

  The Blastz-net alignments have been updated for the following species.
  Read more...

General News

• Canonical Transcripts
  

  Canonical transcripts have been defined for all genes in the core databases.
  Read more...

More news...

Statistics

How the statistics are calculated