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Muscovy Duck (domestic type) assembly and gene annotation

Assembly

The CaiMos1.0 assembly was submitted by McDonnell Genome Institute - Washington University School of Medicine on January 2020. The assembly is on chromosome level, consisting of 30,424 contigs assembled into 3,703 scaffolds. From these sequences, 29 chromosomes have been built. 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 89,133 while the scaffold N50 is 2,417,665.

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

AssemblyCaiMos1.0, INSDC Assembly GCA_009194515.1, Nov 2019
Base Pairs1,109,207,201
Golden Path Length1,109,207,201
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2020
Genebuild releasedMay 2020
Genebuild last updated/patchedFeb 2020
Database version101.1

Gene counts

Coding genes15,898
Non coding genes1,651
Small non coding genes392
Long non coding genes1,256
Misc non coding genes3
Pseudogenes65
Gene transcripts31,625

Other

Genscan gene predictions49,732

About this species

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