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)
9 rows where phylum = "Rotifera" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
Suggested facets: family, order, n_minor_introns, busco_score, minor_snRNAs, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1234261 | Didymodactylos carnosus | Philodinidae | Philodinida | Rotifera | GCA_905250885.1 | 62 | 151453 | 0.0409200409200409 | 88.2 | ["u11", "u12", "u4atac", "u6atac"] | Dc_DCAR706_reference_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/885/GCA_905250885.1_Dc_DCAR706_reference_genomic_v1 | GCA_905250885.1;PRJEB43239;SAMEA8117360;CAJNOQ000000000.1;representative genome;1234261;1234261;Didymodactylos carnosus;;;latest;Scaffold;Major;Full;2021/03/21;Dc_DCAR706_reference_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/885/GCA_905250885.1_Dc_DCAR706_reference_genomic_v1;;;na | 1 |
| 249248 | Adineta ricciae | Adinetidae | Adinetida | Rotifera | GCA_905250025.1 | 18 | 199094 | 0.0090401382136686 | 96.5 | ["u11", "u12", "u4atac", "u6atac"] | Ar_ARIC003_reference_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/025/GCA_905250025.1_Ar_ARIC003_reference_genomic_v1 | GCA_905250025.1;PRJEB43239;SAMEA8117355;CAJNOJ000000000.1;representative genome;249248;249248;Adineta ricciae;;;latest;Scaffold;Major;Full;2021/03/19;Ar_ARIC003_reference_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/025/GCA_905250025.1_Ar_ARIC003_reference_genomic_v1;;;na | 1 |
| 2762512 | Rotaria sp. silwood2 | Rotifera | GCA_905329745.1 | 12 | 140560 | 0.0085365506644281 | 88.6 | ["u11", "u12", "u4atac", "u6atac"] | Rp_RPSE411_reference_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/329/745/GCA_905329745.1_Rp_RPSE411_reference_genomic_v1 | GCA_905329745.1;PRJEB43239;SAMEA8117369;CAJNSZ000000000.1;representative genome;2762512;2762512;Rotaria sp. Silwood2;;;latest;Scaffold;Major;Full;2021/03/20;Rp_RPSE411_reference_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/329/745/GCA_905329745.1_Rp_RPSE411_reference_genomic_v1;;;na | 1 | ||
| 104778 | Seison nebaliae | Seisonidae | Seisonacea | Rotifera | GCA_023231475.1 | 3 | 38785 | 0.0077343508301536 | 75.7 | ["u12", "u4atac", "u6atac"] | GA2.2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/231/475/GCA_023231475.1_GA2.2 | GCA_023231475.1;PRJEB43415;SAMN27400648;JALJEE000000000.1;representative genome;104778;104778;Seison nebaliae;;594-2016;latest;Contig;Major;Full;2022/05/03;GA2.2;Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/231/475/GCA_023231475.1_GA2.2;;;na | 1 |
| 104782 | Adineta vaga | Adinetidae | Adinetida | Rotifera | GCA_021613535.1 | 10 | 137682 | 0.0072625860616448 | 94.5 | ["u11", "u12", "u4atac", "u6atac"] | ASM2161353v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/613/535/GCA_021613535.1_ASM2161353v1 | GCA_021613535.1;PRJNA680543;SAMN16913262;;representative genome;104782;104782;Adineta vaga;breed=AD008;;latest;Chromosome;Major;Full;2022/01/26;ASM2161353v1;University of Namur;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/613/535/GCA_021613535.1_ASM2161353v1;genome length too small;;na | 1 |
| 392033 | Rotaria sordida | Rotifera | GCA_905250125.1 | 18 | 249451 | 0.0072153253510456 | 93.7 | ["u11", "u12", "u4atac", "u6atac"] | Rd_10x_megabubbles_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/125/GCA_905250125.1_Rd_10x_megabubbles_genomic_v1 | GCA_905250125.1;PRJEB43238;SAMEA8116335;CAJNOL000000000.1;representative genome;392033;392033;Rotaria sordida;;;latest;Scaffold;Major;Full;2021/03/21;Rd_10x_megabubbles_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/125/GCA_905250125.1_Rd_10x_megabubbles_genomic_v1;;;na | 1 | ||
| 2762511 | Rotaria sp. silwood1 | Rotifera | GCA_905250075.1 | 14 | 272398 | 0.0051392743344639 | 96.5 | ["u11", "u12", "u4atac", "u6atac"] | Rw_10x_megabubbles_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/075/GCA_905250075.1_Rw_10x_megabubbles_genomic_v1 | GCA_905250075.1;PRJEB43238;SAMEA8116333;CAJNOP000000000.1;representative genome;2762511;2762511;Rotaria sp. Silwood1;;;latest;Scaffold;Major;Full;2021/03/21;Rw_10x_megabubbles_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/075/GCA_905250075.1_Rw_10x_megabubbles_genomic_v1;;;na | 1 | ||
| 433720 | Adineta steineri | Adinetidae | Adinetida | Rotifera | GCA_905250115.1 | 6 | 185078 | 0.0032417713038404 | 92.2 | ["u11", "u12", "u4atac", "u6atac"] | As_10x_pseudohap_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/115/GCA_905250115.1_As_10x_pseudohap_genomic_v1 | GCA_905250115.1;PRJEB43239;SAMEA8116334;CAJNOI000000000.1;representative genome;433720;433720;Adineta steineri;;;latest;Scaffold;Major;Full;2021/03/20;As_10x_pseudohap_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/250/115/GCA_905250115.1_As_10x_pseudohap_genomic_v1;;;na | 1 |
| 392032 | Rotaria socialis | Rotifera | GCA_905331475.1 | 3 | 133999 | 0.0022387725556334 | 96.1 | ["u11", "u12", "u4atac", "u6atac"] | Rs_AK16_reference_genomic_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/331/475/GCA_905331475.1_Rs_AK16_reference_genomic_v1 | GCA_905331475.1;PRJEB43239;SAMEA8117379;CAJNYU000000000.1;representative genome;392032;392032;Rotaria socialis;;;latest;Scaffold;Major;Full;2021/03/19;Rs_AK16_reference_genomic_v1;IMPERIAL COLLEGE LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/331/475/GCA_905331475.1_Rs_AK16_reference_genomic_v1;;;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]);