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Indian glassy fish assembly and gene annotation

Assembly

The fParRan2.1 assembly was submitted by SC on February 2019. The assembly is on chromosome level, consisting of 1,677 contigs assembled into 156 scaffolds. From these sequences, 22 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 5,080,925 while the scaffold N50 is 22,993,012.

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

AssemblyfParRan2.1, INSDC Assembly GCA_900634625.1, Feb 2019
Base Pairs551,012,959
Golden Path Length551,012,959
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedMay 2019
Database version100.21

Gene counts

Coding genes23,965
Non coding genes2,208
Small non coding genes954
Long non coding genes1,247
Misc non coding genes7
Pseudogenes515
Gene transcripts60,337

Other

Genscan gene predictions33,760

About this species

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