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 48

Ochotona princeps News

• New species - American Pika
  This release sees the addition of another 2x genome, the American Pika (Ochotona princeps).
  Read more...

General News

• Change to SliceAdaptor
  The method fetch_by_region() in Bio::EnsEMBL::DBSQL::SliceAdaptor has an additional optional argument $no_fuzz which, if set to a true value, will ensure that the fuzzy matching is not performed when no exact match for the given $seq_region_name is found.
  Read more...
• Variation API
  AlignStrainSlice has been extended to handle insertions/deletions in the particular individual/strain.
• miRNA updates
  All chordate species have been brought up-to-date with version 10.0 of miRBase.
• GO term projections
  

  For this release we have further increased the number of inter-species GO-term projections.
  Read more...

More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions