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Mainland tiger snake assembly and gene annotation

Assembly

The TS10Xv2-PRI assembly was submitted by University Of New South Wales on September 2018. The assembly is on scaffold level, consisting of 131,885 contigs assembled into 52,414 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 31,763 while the scaffold N50 is 5,997,050.

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

AssemblyTS10Xv2-PRI, INSDC Assembly GCA_900518725.1, Sep 2018
Base Pairs1,665,525,958
Golden Path Length1,665,525,958
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedOct 2018
Genebuild releasedApr 2019
Genebuild last updated/patchedDec 2018
Database version100.2

Gene counts

Coding genes18,969
Non coding genes1,566
Small non coding genes715
Long non coding genes655
Misc non coding genes196
Pseudogenes104
Gene transcripts30,892

Other

Genscan gene predictions134,268

About this species

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