Rufous-capped babbler (ASM869450v1)

Rufous-capped babbler assembly and gene annotation

Assembly

The ASM869450v1 assembly was submitted by Academia Sinica on September 2019. The assembly is on scaffold level, consisting of 20,101 contigs assembled into 7,756 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 194,313 while the scaffold N50 is 15,643,638.

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

AssemblyASM869450v1, INSDC Assembly GCA_008694505.1, Sep 2019
Base Pairs1,041,446,934
Golden Path Length1,041,446,934
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2019
Genebuild releasedApr 2020
Genebuild last updated/patchedDec 2019
Database version111.1

Gene counts

Coding genes15,303
Non coding genes593
Small non coding genes369
Long non coding genes223
Misc non coding genes1
Pseudogenes79
Gene transcripts22,341

Other

Genscan gene predictions39,309