This release features the first draft assembly of the mallard duck (Anas platyrhynchos) genome, BGI_duck_1.0, submitted by the State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing in April 2013. The assembly comprises 78487 toplevel sequences, all of which are unplaced scaffolds (from 227448 contigs). The N50 of the contigs is 26 kb and the N50 of the scaffolds is 1.2 Mb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000355885.1
Annotation was performed using the EnsEMBL annotation pipeline, with the gene set being supplemented by the projection of orthologous genes and the inclusion of genes based on alignments with lower coverage than usual. The gene set contains 15,634 protein coding genes, 249 pseudogenes and 567 ncRNAs.
General information about this species can be found in Wikipedia.
|Assembly||BGI_duck_1.0, INSDC Assembly GCA_000355885.1, Apr 2013|
|Golden Path Length|
The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).
|Genebuild method||Full genebuild|
|Genebuild started||Sep 2009|
|Genebuild released||Feb 2010|
|Genebuild last updated/patched||Feb 2010|
Genes and/or transcript that contains an open reading frame (ORF).
|Non coding genes||567|
|Small non coding genes|
Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.
|Misc non coding genes||24|
A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.
|Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.||17,169|
|Genscan gene predictions||42,822|