Chinook salmon (Otsh_v1.0)

Chinook salmon assembly and gene annotation

Assembly

The Otsh_v1.0 assembly was submitted by Fisheries and Oceans Canada on January 2018. The assembly is on chromosome level, consisting of 69,485 contigs assembled into 15,946 scaffolds. From these sequences, 34 chromosomes have been built. 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 the contigs is 133,169 while the scaffold N50 is 1,728,323.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyOtsh_v1.0, INSDC Assembly GCA_002872995.1, Jan 2018
Base Pairs2,425,713,975
Golden Path Length2,425,713,975
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedDec 2019
Database version111.1

Gene counts

Coding genes42,415
Non coding genes4,823
Small non coding genes1,376
Long non coding genes3,424
Misc non coding genes23
Pseudogenes760
Gene transcripts113,653

Other

Genscan gene predictions71,948