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 = "Ascomycota" 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 138285 | Aspergillus coremiiformis | Aspergillaceae | Eurotiales | Ascomycota | GCA_009193565.1 | 4 | 20292 | 0.0197083169097359 | 98.4 | ["u4atac", "u6atac"] | Aspcor1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/193/565/GCA_009193565.1_Aspcor1 | GCA_009193565.1;PRJNA333900;SAMN05446844;STFN00000000.1;representative genome;138285;138285;Aspergillus coremiiformis;strain=CBS 553.77;;latest;Scaffold;Major;Full;2019/10/18;Aspcor1;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/193/565/GCA_009193565.1_Aspcor1;;assembly from type material;na | 1 |
| 1330020 | Ophiocordyceps polyrhachis-furcata | Ophiocordycipitaceae | Hypocreales | Ascomycota | GCA_001633055.2 | 4 | 22951 | 0.0174253975168808 | 93.7 | ["u12", "u6atac"] | OPF BCC54312 improved | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/633/055/GCA_001633055.2_OPF_BCC54312_improved | GCA_001633055.2;PRJNA200756;SAMN04099149;LKCN00000000.2;representative genome;1330021;1330020;Ophiocordyceps polyrhachis-furcata BCC 54312;strain=BCC 54312;;latest;Scaffold;Major;Full;2018/07/17;OPF BCC54312 improved;National Center for Genetic Engineering and Biotechnology (BIOTEC);na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/633/055/GCA_001633055.2_OPF_BCC54312_improved;;;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]);