Pink-footed goose (ASM259213v1)

Pink-footed goose assembly and gene annotation

Assembly

The ASM259213v1 assembly was submitted by Aarhus University, Denmark on October 2017. The assembly is on scaffold level, consisting of 28,533 contigs assembled into 2,723 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 97,462 while the scaffold N50 is 4,974,386.

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

AssemblyASM259213v1, INSDC Assembly GCA_002592135.1, Oct 2017
Base Pairs1,116,992,394
Golden Path Length1,116,992,394
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedDec 2018
Database version111.1

Gene counts

Coding genes15,545
Non coding genes7,040
Small non coding genes434
Long non coding genes6,476
Misc non coding genes130
Pseudogenes56
Gene transcripts38,148

Other

Genscan gene predictions42,647