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)
13 rows where phylum = "Cnidaria" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
Suggested facets: family, order, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 46731 | Pocillopora damicornis | Pocilloporidae | Scleractinia | Cnidaria | GCF_003704095.1 | 633 | 144761 | 0.4353687222306284 | 88.6 | ["u11", "u12", "u4atac", "u6atac"] | ASM370409v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/704/095/GCF_003704095.1_ASM370409v1 | GCF_003704095.1;PRJNA506040;SAMN09007954;RCHS00000000.1;representative genome;46731;46731;Pocillopora damicornis;;RSMAS;latest;Scaffold;Major;Full;2018/10/31;ASM370409v1;University of Miami;GCA_003704095.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/704/095/GCF_003704095.1_ASM370409v1;;;na | 1 |
| 48498 | Orbicella faveolata | Merulinidae | Scleractinia | Cnidaria | GCF_002042975.1 | 658 | 153770 | 0.4260885331675602 | 87.1 | ["u11", "u12", "u4atac", "u6atac"] | ofav_dov_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/042/975/GCF_002042975.1_ofav_dov_v1 | GCF_002042975.1;PRJNA381078;SAMN06562666;MZGG00000000.1;representative genome;48498;48498;Orbicella faveolata;;FL;latest;Scaffold;Major;Full;2017/03/20;ofav_dov_v1;Smithsonian Tropical Research Institute;GCA_002042975.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/042/975/GCF_002042975.1_ofav_dov_v1;;;na | 1 |
| 45351 | Nematostella vectensis | Edwardsiidae | Actiniaria | Cnidaria | GCF_000209225.1 | 682 | 163077 | 0.4164656599026618 | 93.7 | ["u11", "u12", "u4atac", "u6atac"] | ASM20922v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/209/225/GCF_000209225.1_ASM20922v1 | GCF_000209225.1;PRJNA19965;SAMN02953687;ABAV00000000.1;representative genome;45351;45351;Nematostella vectensis;strain=CH2 x CH6;;latest;Scaffold;Major;Full;2007/08/22;ASM20922v1;DOE Joint Genome Institute (JGI);GCA_000209225.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/209/225/GCF_000209225.1_ASM20922v1;;;na | 1 |
| 6105 | Actinia tenebrosa | Actiniidae | Actiniaria | Cnidaria | GCF_009602425.1 | 609 | 146062 | 0.4152150050112156 | 95.3 | ["u11", "u12", "u4atac", "u6atac"] | ASM960242v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/602/425/GCF_009602425.1_ASM960242v1 | GCF_009602425.1;PRJNA590223;SAMN10439458;WAHB00000000.1;representative genome;6105;6105;Actinia tenebrosa;;;latest;Scaffold;Major;Full;2019/11/06;ASM960242v1;QUT;GCA_009602425.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/602/425/GCF_009602425.1_ASM960242v1;;;na | 1 |
| 2652724 | Exaiptasia diaphana | Aiptasiidae | Actiniaria | Cnidaria | GCF_001417965.1 | 590 | 142729 | 0.4116690738841326 | 93.3 | ["u11", "u12", "u4atac", "u6atac"] | Aiptasia genome 1.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/417/965/GCF_001417965.1_Aiptasia_genome_1.1 | GCF_001417965.1;PRJNA386175;SAMN03839803;LJWW00000000.1;representative genome;2652724;2652724;Exaiptasia diaphana;;CC7;latest;Scaffold;Major;Full;2015/10/28;Aiptasia genome 1.1;KAUST;GCA_001417965.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/417/965/GCF_001417965.1_Aiptasia_genome_1.1;;;na | 1 |
| 50429 | Stylophora pistillata | Pocilloporidae | Scleractinia | Cnidaria | GCF_002571385.1 | 637 | 165556 | 0.383289308213944 | 90.6 | ["u11", "u12", "u4atac", "u6atac"] | Stylophora pistillata v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/571/385/GCF_002571385.1_Stylophora_pistillata_v1 | GCF_002571385.1;PRJNA415215;SAMN03491624;LSMT00000000.1;representative genome;50429;50429;Stylophora pistillata;;CSM Monaco;latest;Scaffold;Major;Full;2017/10/17;Stylophora pistillata v1;KAUST;GCA_002571385.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/571/385/GCF_002571385.1_Stylophora_pistillata_v1;;;na | 1 |
| 151771 | Dendronephthya gigantea | Nephtheidae | Alcyonacea | Cnidaria | GCF_004324835.1 | 638 | 169687 | 0.3745780126229268 | 98.0 | ["u11", "u12", "u4atac", "u6atac"] | DenGig_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/324/835/GCF_004324835.1_DenGig_1.0 | GCF_004324835.1;PRJNA529494;SAMN10516674;RSEI00000000.1;representative genome;151771;151771;Dendronephthya gigantea;;DGI-Jeju-01;latest;Contig;Major;Full;2019/03/04;DenGig_1.0;Ulsan National Institute of Science and Technology;GCA_004324835.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/324/835/GCF_004324835.1_DenGig_1.0;;;na | 1 |
| 45264 | Acropora millepora | Acroporidae | Scleractinia | Cnidaria | GCF_013753865.1 | 721 | 193229 | 0.3717452951791699 | 97.3 | ["u11", "u12", "u4atac", "u6atac"] | Amil_v2.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/753/865/GCF_013753865.1_Amil_v2.1 | GCF_013753865.1;PRJNA767661;SAMN14973899;JACAWQ000000000.1;representative genome;45264;45264;Acropora millepora;;JS-1;latest;Chromosome;Major;Full;2020/07/29;Amil_v2.1;Columbia;GCA_013753865.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/753/865/GCF_013753865.1_Amil_v2.1;;;na | 1 |
| 70779 | Acropora digitifera | Acroporidae | Scleractinia | Cnidaria | GCF_000222465.1 | 559 | 150659 | 0.3696649869724503 | 75.3 | ["u11", "u12", "u4atac", "u6atac"] | Adig_1.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/222/465/GCF_000222465.1_Adig_1.1 | GCF_000222465.1;PRJNA314803;SAMD00004206;BACK00000000.2;representative genome;70779;70779;Acropora digitifera;;;latest;Scaffold;Major;Full;2016/01/15;Adig_1.1;Okinawa Institute of Science and Technology;GCA_000222465.2;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/222/465/GCF_000222465.1_Adig_1.1;;;na | 1 |
| 2897299 | Xenia sp. carnegie-2017 | Xeniidae | Alcyonacea | Cnidaria | GCF_021976095.1 | 553 | 150473 | 0.3661621177810443 | 96.9 | ["u11", "u12", "u4atac", "u6atac"] | XeniaSp_v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/976/095/GCF_021976095.1_XeniaSp_v1 | GCF_021976095.1;PRJNA809689;SAMN23741995;JAJSDR000000000.1;representative genome;2897299;2897299;Xenia sp. Carnegie-2017;;Carnegie-2017;latest;Scaffold;Major;Full;2022/02/04;XeniaSp_v1;Carnegie Institution of Washington;GCA_021976095.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/976/095/GCF_021976095.1_XeniaSp_v1;;;na | 1 |
| 6106 | Actinia equina | Actiniidae | Actiniaria | Cnidaria | GCA_011057435.1 | 700 | 230025 | 0.3033914833676455 | 95.7 | ["u11", "u12", "u4atac", "u6atac"] | equina_smartden.arrow4.noredun | ftp://ftp.ensemblgenomes.org/pub/metazoa/release-51/fasta/actinia_equina_gca011057435/dna/Actinia_equina_gca011057435.equina_smartden.arrow4.noredun.dna.toplevel.fa.gz; ftp://ftp.ensemblgenomes.org/pub/metazoa/release-51/gtf/actinia_equina_gca011057435/Actinia_equina_gca011057435.equina_smartden.arrow4.noredun.51.gtf.gz | Actinia equina (AE1) - GCA_011057435.1;actinia_equina_gca011057435;EnsemblMetazoa;6106;equina_smartden.arrow4.noredun;GCA_011057435.1;equinasmartdenvarrow4vnoredun.0;N;N;N;Y;N;Y;actinia_equina_gca011057435_core_51_104_1;1 | 1 |
| 6087 | Hydra vulgaris | Hydridae | Anthoathecata | Cnidaria | GCF_022113875.1 | 317 | 141713 | 0.2231922833204252 | 98.4 | ["u11", "u12", "u4atac", "u6atac"] | Hydra_105_v3 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/022/113/875/GCF_022113875.1_Hydra_105_v3 | GCF_022113875.1;PRJNA814716;SAMN18321928;JAGKSS000000000.1;representative genome;6087;6087;Hydra vulgaris;;105;latest;Chromosome;Major;Full;2022/02/14;Hydra_105_v3;University of Vienna;GCA_022113875.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/022/113/875/GCF_022113875.1_Hydra_105_v3;;;na | 1 |
| 252671 | Clytia hemisphaerica | Clytiidae | Leptothecata | Cnidaria | GCA_902728285.1 | 274 | 131705 | 0.2076087862462967 | 83.1 | ["u11", "u12", "u4atac", "u6atac"] | GCA902728285v1 | ftp://ftp.ensemblgenomes.org/pub/metazoa/release-51/fasta/clytia_hemisphaerica_gca902728285/dna/Clytia_hemisphaerica_gca902728285.GCA902728285v1.dna.toplevel.fa.gz; ftp://ftp.ensemblgenomes.org/pub/metazoa/release-51/gtf/clytia_hemisphaerica_gca902728285/Clytia_hemisphaerica_gca902728285.GCA902728285v1.51.gtf.gz | Clytia hemisphaerica (Z4C2);clytia_hemisphaerica_gca902728285;EnsemblMetazoa;252671;GCA902728285v1;GCA_902728285.1;GCA902728285v1.0;N;N;N;Y;N;Y;clytia_hemisphaerica_gca902728285_core_51_104_1;1 | 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]);