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)
25 rows where minor_snRNAs = "["u12", "u6atac"]" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
Suggested facets: family, order, phylum, n_minor_introns, busco_score, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 187382 | Chlamydotis macqueenii | Otididae | Gruiformes | Chordata | GCF_000695195.1 | 433 | 112937 | 0.381935256240628 | 60.0 | ["u12", "u6atac"] | ASM69519v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/695/195/GCF_000695195.1_ASM69519v1 | GCF_000695195.1;PRJNA266006;SAMN02324157;JMFJ00000000.1;representative genome;187382;187382;Chlamydotis macqueenii;;BGI_N324;latest;Scaffold;Major;Full;2014/06/02;ASM69519v1;BGI;GCA_000695195.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/695/195/GCF_000695195.1_ASM69519v1;;;na | 1 |
| 925459 | Balearica regulorum | Gruidae | Gruiformes | Chordata | GCF_000709895.1 | 450 | 118975 | 0.376805526481055 | 60.8 | ["u12", "u6atac"] | ASM70989v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/709/895/GCF_000709895.1_ASM70989v1 | GCF_000709895.1;PRJNA264996;SAMN02318095;JJRR00000000.1;representative genome;100784;925459;Balearica regulorum gibbericeps;;BGI_N312;latest;Scaffold;Major;Full;2014/06/25;ASM70989v1;BGI;GCA_000709895.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/709/895/GCF_000709895.1_ASM70989v1;;;na | 1 |
| 37040 | Gavia stellata | Gaviidae | Gaviiformes | Chordata | GCF_000690875.1 | 420 | 112258 | 0.3727435701734145 | 61.6 | ["u12", "u6atac"] | ASM69087v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/690/875/GCF_000690875.1_ASM69087v1 | GCF_000690875.1;PRJNA261843;SAMN02324832;JJRM00000000.1;representative genome;37040;37040;Gavia stellata;;BGI_N328;latest;Scaffold;Major;Full;2014/05/13;ASM69087v1;BGI;GCA_000690875.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/690/875/GCF_000690875.1_ASM69087v1;;;na | 1 |
| 57421 | Merops nubicus | Meropidae | Coraciiformes | Chordata | GCF_000691845.1 | 408 | 109553 | 0.3710406416820509 | 56.1 | ["u12", "u6atac"] | ASM69184v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/691/845/GCF_000691845.1_ASM69184v1 | GCF_000691845.1;PRJNA253837;SAMN02338310;JJRJ00000000.1;representative genome;57421;57421;Merops nubicus;;BGI_N331;latest;Scaffold;Major;Full;2014/05/16;ASM69184v1;BGI;GCA_000691845.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/691/845/GCF_000691845.1_ASM69184v1;;;na | 1 |
| 57412 | Colius striatus | Coliidae | Coliiformes | Chordata | GCF_000690715.1 | 408 | 109695 | 0.37056211002425 | 60.0 | ["u12", "u6atac"] | ASM69071v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/690/715/GCF_000690715.1_ASM69071v1 | GCF_000690715.1;PRJNA265879;SAMN02324230;JJRP00000000.1;representative genome;57412;57412;Colius striatus;;BGI_N325;latest;Scaffold;Major;Full;2014/05/13;ASM69071v1;BGI;GCA_000690715.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/690/715/GCF_000690715.1_ASM69071v1;;;na | 1 |
| 121530 | Tauraco erythrolophus | Musophagidae | Musophagiformes | Chordata | GCF_000709365.1 | 438 | 117995 | 0.3698293549939628 | 62.7 | ["u12", "u6atac"] | ASM70936v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/709/365/GCF_000709365.1_ASM70936v1 | GCF_000709365.1;PRJNA265115;SAMN02339893;JNOY00000000.1;representative genome;121530;121530;Tauraco erythrolophus;;BGI_N340;latest;Scaffold;Major;Full;2014/06/25;ASM70936v1;BGI;GCA_000709365.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/709/365/GCF_000709365.1_ASM70936v1;;;na | 1 |
| 97097 | Phaethon lepturus | Phaethontidae | Pelecaniformes | Chordata | GCF_000687285.1 | 439 | 118622 | 0.3687185560343017 | 66.7 | ["u12", "u6atac"] | ASM68728v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/687/285/GCF_000687285.1_ASM68728v1 | GCF_000687285.1;PRJNA265998;SAMN02339888;JJRF00000000.1;representative genome;97097;97097;Phaethon lepturus;;BGI_N335;latest;Scaffold;Major;Full;2014/05/08;ASM68728v1;BGI;GCA_000687285.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/687/285/GCF_000687285.1_ASM68728v1;;;na | 1 |
| 54380 | Cariama cristata | Cariamidae | Cariamiformes | Chordata | GCF_000690535.1 | 435 | 118570 | 0.3655308600478971 | 61.6 | ["u12", "u6atac"] | ASM69053v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/690/535/GCF_000690535.1_ASM69053v1 | GCF_000690535.1;PRJNA263623;SAMN02318733;JJRQ00000000.1;representative genome;54380;54380;Cariama cristata;;BGI_N322;latest;Scaffold;Major;Full;2014/05/12;ASM69053v1;BGI;GCA_000690535.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/690/535/GCF_000690535.1_ASM69053v1;;;na | 1 |
| 279965 | Antrostomus carolinensis | Caprimulgidae | Caprimulgiformes | Chordata | GCF_000700745.1 | 419 | 114394 | 0.3649412522972137 | 55.3 | ["u12", "u6atac"] | ASM70074v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/700/745/GCF_000700745.1_ASM70074v1 | GCF_000700745.1;PRJNA265383;SAMN02318612;JMFU00000000.1;representative genome;279965;279965;Antrostomus carolinensis;;BGI_N321;latest;Scaffold;Major;Full;2014/06/10;ASM70074v1;BGI;GCA_000700745.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/700/745/GCF_000700745.1_ASM70074v1;;;na | 1 |
| 175835 | Buceros rhinoceros | Bucerotidae | Bucerotiformes | Chordata | GCF_000710305.1 | 419 | 115044 | 0.3628868122255614 | 61.6 | ["u12", "u6atac"] | ASM71030v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/710/305/GCF_000710305.1_ASM71030v1 | GCF_000710305.1;PRJNA266010;SAMN02318191;JMFK00000000.1;representative genome;175836;175835;Buceros rhinoceros silvestris;;BGI_N320;latest;Scaffold;Major;Full;2014/06/25;ASM71030v1;BGI;GCA_000710305.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/710/305/GCF_000710305.1_ASM71030v1;;;na | 1 |
| 240206 | Pterocles gutturalis | Pteroclidae | Ciconiiformes | Chordata | GCF_000699245.1 | 408 | 113344 | 0.3586750123074759 | 64.7 | ["u12", "u6atac"] | ASM69924v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/245/GCF_000699245.1_ASM69924v1 | GCF_000699245.1;PRJNA265368;SAMN02339892;JMFR00000000.1;representative genome;240206;240206;Pterocles gutturalis;;BGI_N339;latest;Scaffold;Major;Full;2014/06/09;ASM69924v1;BGI;GCA_000699245.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/699/245/GCF_000699245.1_ASM69924v1;;;na | 1 |
| 8897 | Chaetura pelagica | Apodidae | Apodiformes | Chordata | GCF_000747805.1 | 496 | 138981 | 0.3556141872853589 | 87.8 | ["u12", "u6atac"] | ChaPel_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/747/805/GCF_000747805.1_ChaPel_1.0 | GCF_000747805.1;PRJNA264987;SAMN03018471;AVOS00000000.1;representative genome;8897;8897;Chaetura pelagica;;M959;latest;Scaffold;Major;Full;2014/09/04;ChaPel_1.0;BGI;GCA_000747805.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/747/805/GCF_000747805.1_ChaPel_1.0;;;na | 1 |
| 188379 | Egretta garzetta | Ardeidae | Pelecaniformes | Chordata | GCF_000687185.1 | 498 | 143452 | 0.3459534560611323 | 82.7 | ["u12", "u6atac"] | ASM68718v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/687/185/GCF_000687185.1_ASM68718v1 | GCF_000687185.1;PRJNA253831;SAMN02596466;JJRC00000000.1;representative genome;188379;188379;Egretta garzetta;;BGI_Z169;latest;Scaffold;Major;Full;2014/05/09;ASM68718v1;College of Medicine and Forensics, Xi'an Jiaotong University;GCA_000687185.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/687/185/GCF_000687185.1_ASM68718v1;;;na | 1 |
| 8801 | Struthio camelus | Struthionidae | Struthioniformes | Chordata | GCF_000698965.1 | 518 | 150944 | 0.3419999735907356 | 87.1 | ["u12", "u6atac"] | ASM69896v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/698/965/GCF_000698965.1_ASM69896v1 | GCF_000698965.1;PRJNA263340;SAMN02316164;JJRT00000000.1;representative genome;441894;8801;Struthio camelus australis;;BGI_N308;latest;Scaffold;Major;Full;2014/06/06;ASM69896v1;BGI;GCA_000698965.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/698/965/GCF_000698965.1_ASM69896v1;;;na | 1 |
| 194338 | Athene cunicularia | Strigidae | Strigiformes | Chordata | GCF_003259725.1 | 506 | 147452 | 0.3419889428080942 | 87.1 | ["u12", "u6atac"] | athCun1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/259/725/GCF_003259725.1_athCun1 | GCF_003259725.1;PRJNA497593;SAMN08961563;QEEU00000000.1;representative genome;194338;194338;Athene cunicularia;;RWA;latest;Scaffold;Major;Full;2018/06/21;athCun1;Stefan Boerno's shared submissions;GCA_003259725.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/259/725/GCF_003259725.1_athCun1;;;na | 1 |
| 8845 | Anser cygnoides | Anatidae | Anseriformes | Chordata | GCF_000971095.1 | 524 | 163163 | 0.3201231618882379 | 84.3 | ["u12", "u6atac"] | AnsCyg_PRJNA183603_v1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/971/095/GCF_000971095.1_AnsCyg_PRJNA183603_v1.0 | GCF_000971095.1;PRJNA290577;SAMN01830643;AOGC00000000.1;representative genome;381198;8845;Anser cygnoides domesticus;breed=Zhedong;;latest;Scaffold;Major;Full;2015/04/08;AnsCyg_PRJNA183603_v1.0;Anser cygnoides Genome consortium;GCA_000971095.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/971/095/GCF_000971095.1_AnsCyg_PRJNA183603_v1.0;;;na | 1 |
| 345573 | Podiceps cristatus | Podicipedidae | Podicipediformes | Chordata | GCA_000699545.1 | 193 | 64760 | 0.2971379305035949 | 60.8 | ["u12", "u6atac"] | ASM69954v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/699/545/GCA_000699545.1_ASM69954v1 | GCA_000699545.1;PRJNA212905;SAMN02339891;JMFS00000000.1;representative genome;345573;345573;Podiceps cristatus;;BGI_N338;latest;Scaffold;Major;Full;2014/06/11;ASM69954v1;BGI;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/699/545/GCA_000699545.1_ASM69954v1;;;na | 1 |
| 1977171 | Nothocercus nigrocapillus | Tinamidae | Tinamiformes | Chordata | GCA_013398345.1 | 290 | 104429 | 0.2769315978953198 | 81.6 | ["u12", "u6atac"] | ASM1339834v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/345/GCA_013398345.1_ASM1339834v1 | GCA_013398345.1;PRJNA545868;SAMN12253973;WBNA00000000.1;representative genome;1977171;1977171;Nothocercus nigrocapillus;;B10K-MSB-02;latest;Scaffold;Major;Full;2020/07/10;ASM1339834v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/345/GCA_013398345.1_ASM1339834v1;;;na | 1 |
| 2585814 | Nothoprocta pentlandii | Tinamidae | Tinamiformes | Chordata | GCA_013398315.1 | 296 | 106621 | 0.276850267029565 | 82.0 | ["u12", "u6atac"] | ASM1339831v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/315/GCA_013398315.1_ASM1339831v1 | GCA_013398315.1;PRJNA545868;SAMN12253975;VZSG00000000.1;representative genome;2585814;2585814;Nothoprocta pentlandii;;B10K-MSB-04;latest;Scaffold;Major;Full;2020/07/10;ASM1339831v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/315/GCA_013398315.1_ASM1339831v1;;;na | 1 |
| 2585813 | Nothocercus julius | Tinamidae | Tinamiformes | Chordata | GCA_013398735.1 | 294 | 106904 | 0.2742588481128379 | 85.5 | ["u12", "u6atac"] | ASM1339873v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/735/GCA_013398735.1_ASM1339873v1 | GCA_013398735.1;PRJNA545868;SAMN12253972;VZSV00000000.1;representative genome;2585813;2585813;Nothocercus julius;;B10K-MSB-01;latest;Scaffold;Major;Full;2020/07/10;ASM1339873v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/735/GCA_013398735.1_ASM1339873v1;;;na | 1 |
| 81907 | Alectura lathami | Megapodiidae | Galliformes | Chordata | GCA_013399715.1 | 284 | 105475 | 0.2685350655736155 | 80.8 | ["u12", "u6atac"] | ASM1339971v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/399/715/GCA_013399715.1_ASM1339971v1 | GCA_013399715.1;PRJNA545868;SAMN12253796;VXAV00000000.1;representative genome;81907;81907;Alectura lathami;;B10K-DU-001-39;latest;Scaffold;Major;Full;2020/07/10;ASM1339971v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/399/715/GCA_013399715.1_ASM1339971v1;;;na | 1 |
| 81970 | Arabidopsis halleri | Brassicaceae | Brassicales | Streptophyta | Ahalleri_v1_1 | 253 | 104890 | 0.2406246730643029 | 90.2 | ["u12", "u6atac"] | . | . | 1 | |
| 6689 | Penaeus vannamei | Penaeidae | Decapoda | Arthropoda | GCF_003789085.1 | 103 | 144922 | 0.0710222375452508 | 87.1 | ["u12", "u6atac"] | ASM378908v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/789/085/GCF_003789085.1_ASM378908v1 | GCF_003789085.1;PRJNA508983;SAMN08721527;QCYY00000000.1;representative genome;6689;6689;Penaeus vannamei;breed=Kehai No.1;;latest;Scaffold;Major;Full;2018/11/16;ASM378908v1;Institute of Oceanology, Chinese Academy of Sciences;GCA_003789085.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/789/085/GCF_003789085.1_ASM378908v1;;;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 |
| 139363 | Hydnum rufescens | Hydnaceae | Cantharellales | Basidiomycota | GCA_014904985.1 | 5 | 78054 | 0.006405411291459 | 91.4 | ["u12", "u6atac"] | Hydru2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/904/985/GCA_014904985.1_Hydru2 | GCA_014904985.1;PRJNA234814;SAMN05660910;WIOR00000000.1;representative genome;1448309;139363;Hydnum rufescens UP504;strain=UP504;;latest;Scaffold;Major;Full;2020/10/20;Hydru2;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/904/985/GCA_014904985.1_Hydru2;;;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]);