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Chacoan peccary assembly and gene annotation

Assembly

The CatWag_v2_BIUU_UCD assembly was submitted by Broad Institute on July 2019. The assembly is on scaffold level, consisting of 1,240,743 contigs assembled into 1,183,730 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 65,965 while the scaffold N50 is 19,204,659.

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

AssemblyCatWag_v2_BIUU_UCD, INSDC Assembly GCA_004024745.2, Jul 2019
Base Pairs2,640,067,814
Golden Path Length2,640,067,814
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJul 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedSep 2019
Database version100.2

Gene counts

Coding genes19,627
Non coding genes1,926
Small non coding genes1,859
Long non coding genes51
Misc non coding genes16
Pseudogenes528
Gene transcripts31,963

Other

Genscan gene predictions128,374

About this species

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