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)
2 rows where phylum = "Placozoa" 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10228 | Trichoplax adhaerens | Trichoplacidae | Placozoa | GCF_000150275.1 | 211 | 93076 | 0.2261837126287693 | 94.5 | ["u11", "u12", "u4atac", "u6atac"] | v1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/150/275/GCF_000150275.1_v1.0 | GCF_000150275.1;PRJNA30931;SAMN02953699;ABGP00000000.1;representative genome;10228;10228;Trichoplax adhaerens;strain=Grell-BS-1999;;latest;Scaffold;Major;Full;2008/06/17;v1.0;US DOE Joint Genome Institute (JGI-PGF);GCA_000150275.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/150/275/GCF_000150275.1_v1.0;;;na | 1 | |
| 287889 | Trichoplax sp. h2 | Trichoplacidae | Placozoa | GCA_003344405.1 | 210 | 113910 | 0.1840168243953732 | 96.1 | ["u11", "u12", "u4atac", "u6atac"] | TrispH2_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/344/405/GCA_003344405.1_TrispH2_1.0 | GCA_003344405.1;PRJNA393433;SAMN07333237;NOWV00000000.1;representative genome;287889;287889;Trichoplax sp. H2;strain=Panama;;latest;Scaffold;Major;Full;2018/07/27;TrispH2_1.0;University of Veterinary Medicine Hannover, Foundation;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/344/405/GCA_003344405.1_TrispH2_1.0;;;na | 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]);