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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

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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]);
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