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 = "["u11", "u12", "u4atac"]" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 6500 | Aplysia californica | Aplysiidae | Aplysiida | Mollusca | GCF_000002075.1 | 476 | 141803 | 0.3345539397943477 | 91.4 | ["u11", "u12", "u4atac"] | AplCal3.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/075/GCF_000002075.1_AplCal3.0 | GCF_000002075.1;PRJNA209509;SAMN02953658;AASC00000000.3;representative genome;6500;6500;Aplysia californica;;F4 #8;latest;Scaffold;Major;Full;2013/05/15;AplCal3.0;Broad Institute;GCA_000002075.2;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/075/GCF_000002075.1_AplCal3.0;;;na | 1 |
| 264402 | Capsella grandiflora | Brassicaceae | Brassicales | Streptophyta | Cgrandiflora_v1_1 | 258 | 107885 | 0.2385730005640679 | 95.7 | ["u11", "u12", "u4atac"] | . | . | 1 | |
| 44941 | Gigaspora rosea | Gigasporaceae | Diversisporales | Mucoromycota | GCA_003550325.1 | 190 | 90294 | 0.2099818752486627 | 92.9 | ["u11", "u12", "u4atac"] | ASM355032v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/550/325/GCA_003550325.1_ASM355032v1 | GCA_003550325.1;PRJNA430513;SAMN08375202;QKWP00000000.1;representative genome;44941;44941;Gigaspora rosea;strain=DAOM 194757;;latest;Scaffold;Major;Full;2018/09/12;ASM355032v1;INRA;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/550/325/GCA_003550325.1_ASM355032v1;;;na | 1 |
Advanced export
JSON shape: default, array, newline-delimited, object
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]);