Chinese medaka (ASM858656v1)

Chinese medaka assembly and gene annotation

Assembly

The ASM858656v1 assembly was submitted by Peking University on September 2019. The assembly is on scaffold level, consisting of 98,653 contigs assembled into 68,189 scaffolds. 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 28,180 while the scaffold N50 is 991,358.

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

AssemblyASM858656v1, INSDC Assembly GCA_008586565.1, Sep 2019
Base Pairs813,986,518
Golden Path Length813,986,518
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedDec 2019
Database version111.1

Gene counts

Coding genes21,964
Non coding genes1,277
Small non coding genes362
Long non coding genes899
Misc non coding genes16
Pseudogenes781
Gene transcripts54,551

Other

Genscan gene predictions68,507