genomes
Data license: ODbL · Data source: Larue & Roy, 2023
- taxonomy_id
- INTEGER (primary key), unique identifier for each species
- species
- TEXT, binomial name of the species
- family
- TEXT, taxonomic family of the species
- order
- TEXT, taxonomic order of the species
- phylum
- TEXT, taxonomic phylum of the species
- accession
- TEXT, accession number of the genome assembly
- n_minor_introns
- INTEGER, total number of minor introns in the genome
- n_major_introns
- INTEGER, total number of major introns in the genome
- percent_minor_introns
- REAL, percentage of minor introns in the genome
- busco_score
- REAL, BUSCO score assessing the genome assembly completeness (vs. eukaryota_odb10)
- minor_snRNAs
- TEXT, minor snRNAs found in the annotated transcriptome
- genome_version
- TEXT, version of the genome assembly
- source_url
- TEXT, URL for the source genome/annotation files
- source_metadata
- TEXT, additional metadata from the original data source
- minor_intron+
- INTEGER, indicates if the species is inferred to contain real minor introns (1) or not (0)
1 row where phylum = "Ctenophora" sorted by percent_minor_introns descending
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Suggested facets: minor_snRNAs (array)
| taxonomy_id | species | family | order | phylum | accession | n_minor_introns | n_major_introns | percent_minor_introns ▲ | busco_score | minor_snRNAs | genome_version | source_url | source_metadata | minor_intron+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 27923 | Mnemiopsis leidyi | Bolinopsidae | Lobata | Ctenophora | GCA_000226015.1 | 11 | 74790 | 0.0147056857528642 | 83.5 | ["u11", "u12", "u4atac", "u6atac"] | MneLei_Aug2011 | ftp://ftp.ensemblgenomes.org/pub/metazoa/release-52/fasta/mnemiopsis_leidyi/dna/Mnemiopsis_leidyi.MneLei_Aug2011.dna.toplevel.fa.gz; ftp://ftp.ensemblgenomes.org/pub/metazoa/release-52/gtf/mnemiopsis_leidyi/Mnemiopsis_leidyi.MneLei_Aug2011.52.gtf.gz | Mnemiopsis leidyi;mnemiopsis_leidyi;EnsemblMetazoa;27923;MneLei_Aug2011;GCA_000226015.1;NHGRI v2.2;N;N;Y;Y;N;Y;mnemiopsis_leidyi_core_52_105_1;1 | 1 |
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CREATE TABLE "genomes" (
"taxonomy_id" INTEGER,
"species" TEXT,
"family" TEXT,
"order" TEXT,
"phylum" TEXT,
"accession" TEXT,
"n_minor_introns" INTEGER,
"n_major_introns" INTEGER,
"percent_minor_introns" REAL,
"busco_score" REAL,
"minor_snRNAs" TEXT,
"genome_version" TEXT,
"source_url" TEXT,
"source_metadata" TEXT,
"minor_intron+" INTEGER
,PRIMARY KEY ([taxonomy_id])
);
CREATE INDEX [idx_genomes_phylum]
ON [genomes] ([phylum]);
CREATE INDEX [idx_genomes_order]
ON [genomes] ([order]);
CREATE INDEX [idx_genomes_family]
ON [genomes] ([family]);