Pika assembly and gene annotation


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.

Other assemblies

Gene 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".

Mammalian Genome Project

Ochotona princeps is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.

More information

General information about this species can be found in Wikipedia.



AssemblyOchPri2.0, Jun 2007
Base Pairs1,923,640,532
Golden Path Length4,294,967,295
Annotation methodProjection build
Genebuild startedJan 2008
Genebuild releasedJul 2008
Genebuild last updated/patchedApr 2013
Database version95.1

Gene counts

Coding genes16,006
Gene transcripts23,065


Genscan gene predictions134,260

About this species