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)
3 rows where minor_snRNAs = "["u12", "u4atac"]" sorted by percent_minor_introns descending
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Suggested facets: order, phylum, n_minor_introns, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 74869 | Anopheles maculatus | Culicidae | Diptera | Arthropoda | GCA_000473185.1 | 5 | 24556 | 0.0203574773014128 | 65.9 | ["u12", "u4atac"] | AmacM1 | ftp://ftp.ensemblgenomes.org/pub/metazoa/release-52/fasta/anopheles_maculatus/dna/Anopheles_maculatus.AmacM1.dna.toplevel.fa.gz; ftp://ftp.ensemblgenomes.org/pub/metazoa/release-52/gtf/anopheles_maculatus/Anopheles_maculatus.AmacM1.52.gtf.gz | Anopheles maculatus;anopheles_maculatus;EnsemblMetazoa;74869;AmacM1;GCA_000473185.1;AmacM1.6;N;N;N;Y;Y;Y;anopheles_maculatus_core_52_105_1;1 | 1 |
| 36166 | Megaselia scalaris | Phoridae | Diptera | Arthropoda | GCA_000341915.1 | 3 | 19746 | 0.0151906425641804 | 32.5 | ["u12", "u4atac"] | Msca1 | ftp://ftp.ensemblgenomes.org/pub/metazoa/release-52/fasta/megaselia_scalaris/dna/Megaselia_scalaris.Msca1.dna.toplevel.fa.gz; ftp://ftp.ensemblgenomes.org/pub/metazoa/release-52/gtf/megaselia_scalaris/Megaselia_scalaris.Msca1.52.gtf.gz | Megaselia scalaris;megaselia_scalaris;EnsemblMetazoa;36166;Msca1;GCA_000341915.1;Ensembl Genomes v1.0;N;N;N;Y;N;Y;megaselia_scalaris_core_52_105_1;1 | 1 |
| 32597 | Perkinsus olseni | Perkinsidae | Perkinsida | Perkinsozoa | GCA_013115135.1 | 3 | 114227 | 0.0026262803116519 | 53.7 | ["u12", "u4atac"] | ASM1311513v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/115/135/GCA_013115135.1_ASM1311513v1 | GCA_013115135.1;PRJNA554963;SAMN12288125;JABANP000000000.1;representative genome;32597;32597;Perkinsus olseni;;00978-12;latest;Scaffold;Major;Full;2020/05/18;ASM1311513v1;NSW Department of Primary Industries;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/115/135/GCA_013115135.1_ASM1311513v1;;;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]);