Ring-necked pheasant (ASM414374v1)

Ring-necked pheasant assembly and gene annotation

Assembly

The ASM414374v1 assembly was submitted by Shenzhen University on February 2019. The assembly is on scaffold level, consisting of 58,369 contigs assembled into 39,677 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 197,843 while the scaffold N50 is 10,682,894.

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

AssemblyASM414374v1, INSDC Assembly GCA_004143745.1, Feb 2019
Base Pairs1,017,507,340
Golden Path Length1,017,507,340
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedMar 2020
Database version111.1

Gene counts

Coding genes15,711
Non coding genes6,558
Small non coding genes476
Long non coding genes6,078
Misc non coding genes4
Pseudogenes151
Gene transcripts35,359

Other

Genscan gene predictions40,354