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Yellow-billed parrot assembly and gene annotation

Assembly

The ASM394721v1 assembly was submitted by Weill Cornell Medicine on December 2018. The assembly is on scaffold level, consisting of 22,614 contigs assembled into 10,638 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 208,912 while the scaffold N50 is 13,267,695.

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

AssemblyASM394721v1, INSDC Assembly GCA_003947215.1, Dec 2018
Base Pairs1,258,720,284
Golden Path Length1,258,720,284
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJul 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedSep 2019
Database version100.1

Gene counts

Coding genes16,590
Non coding genes723
Small non coding genes461
Long non coding genes256
Misc non coding genes6
Pseudogenes110
Gene transcripts27,056

Other

Genscan gene predictions44,197

About this species

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