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Golden-collared manakin assembly and gene annotation

Assembly

The ASM171598v2 assembly was submitted by Smithsonian Institution National Museum of Natural History on May 2018. The assembly is on scaffold level, consisting of 29,371 contigs assembled into 15,315 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 194,737 while the scaffold N50 is 16,643,792.

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

AssemblyASM171598v2, INSDC Assembly GCA_001715985.2, May 2018
Base Pairs1,213,150,360
Golden Path Length1,213,150,360
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedDec 2018
Database version100.2

Gene counts

Coding genes15,928
Non coding genes2,590
Small non coding genes413
Long non coding genes2,054
Misc non coding genes123
Pseudogenes103
Gene transcripts30,531

Other

Genscan gene predictions46,800

About this species

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