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)
8 rows where minor_snRNAs = "["u4atac", "u6atac"]" sorted by percent_minor_introns descending
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Suggested facets: family, order, phylum, n_minor_introns, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 94827 | Tinamus guttatus | Tinamidae | Tinamiformes | Chordata | GCF_000705375.1 | 503 | 138386 | 0.3621597102722318 | 76.9 | ["u4atac", "u6atac"] | ASM70537v2 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/705/375/GCF_000705375.1_ASM70537v2 | GCF_000705375.1;PRJNA265201;SAMN02316659;JMFW00000000.2;representative genome;94827;94827;Tinamus guttatus;;BGI_N309;latest;Scaffold;Major;Full;2014/08/05;ASM70537v2;BGI;GCA_000705375.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/705/375/GCF_000705375.1_ASM70537v2;;;na | 1 |
| 43316 | Glareola pratincola | Glareolidae | Charadriiformes | Chordata | GCA_013401295.1 | 285 | 105220 | 0.2701293777546087 | 84.7 | ["u4atac", "u6atac"] | ASM1340129v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/401/295/GCA_013401295.1_ASM1340129v1 | GCA_013401295.1;PRJNA545868;SAMN12253752;VWPO00000000.1;representative genome;43316;43316;Glareola pratincola;;B10K-CU-031-08;latest;Scaffold;Major;Full;2020/07/10;ASM1340129v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/401/295/GCA_013401295.1_ASM1340129v1;;;na | 1 |
| 100268 | Paragonimus heterotremus | Troglotrematidae | Plagiorchiida | Platyhelminthes | GCA_013368495.1 | 83 | 64664 | 0.1281912675490756 | 74.5 | ["u4atac", "u6atac"] | P_heterotremus_1.0.allpaths.pg.lrna | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/368/495/GCA_013368495.1_P_heterotremus_1.0.allpaths.pg.lrna | GCA_013368495.1;PRJNA284523;SAMN04324906;LUCH00000000.1;representative genome;100268;100268;Paragonimus heterotremus;strain=LC;;latest;Scaffold;Major;Full;2020/06/23;P_heterotremus_1.0.allpaths.pg.lrna;McDonnell Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/368/495/GCA_013368495.1_P_heterotremus_1.0.allpaths.pg.lrna;;;na | 1 |
| 100269 | Paragonimus kellicotti | Troglotrematidae | Plagiorchiida | Platyhelminthes | GCA_014220965.1 | 51 | 54311 | 0.0938155329090173 | 63.1 | ["u4atac", "u6atac"] | P_kellicotti_1.0.allpaths.nc.pg.lrna | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/220/965/GCA_014220965.1_P_kellicotti_1.0.allpaths.nc.pg.lrna | GCA_014220965.1;PRJNA179523;SAMN03863379;LOND00000000.1;representative genome;100269;100269;Paragonimus kellicotti;;Missouri;latest;Scaffold;Major;Full;2020/08/17;P_kellicotti_1.0.allpaths.nc.pg.lrna;The Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/220/965/GCA_014220965.1_P_kellicotti_1.0.allpaths.nc.pg.lrna;;;na | 1 |
| 138285 | Aspergillus coremiiformis | Aspergillaceae | Eurotiales | Ascomycota | GCA_009193565.1 | 4 | 20292 | 0.0197083169097359 | 98.4 | ["u4atac", "u6atac"] | Aspcor1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/193/565/GCA_009193565.1_Aspcor1 | GCA_009193565.1;PRJNA333900;SAMN05446844;STFN00000000.1;representative genome;138285;138285;Aspergillus coremiiformis;strain=CBS 553.77;;latest;Scaffold;Major;Full;2019/10/18;Aspcor1;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/193/565/GCA_009193565.1_Aspcor1;;assembly from type material;na | 1 |
| 604196 | Linnemannia exigua | Mortierellaceae | Mortierellales | Mucoromycota | GCA_016097895.1 | 4 | 32839 | 0.0121791553755747 | 92.2 | ["u4atac", "u6atac"] | UCR_MexiNRRL28262_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/097/895/GCA_016097895.1_UCR_MexiNRRL28262_1.0 | GCA_016097895.1;PRJNA340842;SAMN05720535;JAAAIL000000000.1;representative genome;604196;604196;Linnemannia exigua;strain=NRRL 28262;;latest;Scaffold;Major;Full;2020/12/16;UCR_MexiNRRL28262_1.0;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/097/895/GCA_016097895.1_UCR_MexiNRRL28262_1.0;;;na | 1 |
| 64571 | Lobosporangium transversale | Mortierellaceae | Mortierellales | Mucoromycota | GCF_002105155.1 | 3 | 33137 | 0.0090525045262522 | 97.6 | ["u4atac", "u6atac"] | Lobtra1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/105/155/GCF_002105155.1_Lobtra1 | GCF_002105155.1;PRJNA396744;SAMN05421885;MCFF00000000.1;representative genome;64571;64571;Lobosporangium transversale;strain=NRRL 3116;;latest;Contig;Major;Full;2017/04/20;Lobtra1;DOE Joint Genome Institute;GCA_002105155.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/105/155/GCF_002105155.1_Lobtra1;;assembly from type material;na | 1 |
| 64524 | Linnemannia hyalina | Mortierellaceae | Mortierellales | Mucoromycota | GCA_019671135.1 | 3 | 36471 | 0.0082250370126665 | 94.9 | ["u4atac", "u6atac"] | ASM1967113v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/671/135/GCA_019671135.1_ASM1967113v1 | GCA_019671135.1;PRJNA730508;SAMN19232282;JAHRHY000000000.1;representative genome;64524;64524;Linnemannia hyalina;strain=SCG-10;;latest;Contig;Major;Full;2021/08/18;ASM1967113v1;University of Minnesota-Twin Cities;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/671/135/GCA_019671135.1_ASM1967113v1;;;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]);