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Spoon-billed sandpiper assembly and gene annotation

Assembly

The ASM369795v1 assembly was submitted by Adam Mickiewicz University on October 2018. The assembly is on scaffold level, consisting of 44,336 contigs assembled into 29,819 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 189,165 while the scaffold N50 is 3,136,279.

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

AssemblyASM369795v1, INSDC Assembly GCA_003697955.1, Oct 2018
Base Pairs1,178,350,366
Golden Path Length1,178,350,366
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes16,334
Non coding genes2,015
Small non coding genes451
Long non coding genes1,430
Misc non coding genes134
Pseudogenes73
Gene transcripts29,537

Other

Genscan gene predictions51,938

About this species

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