genomes
Data license: ODbL · Data source: Larue & Roy, 2023 · About: Minor Intron Database (WtMTA)
- 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)
4 rows where minor_snRNAs contains "u4atac" and n_minor_introns = 583 sorted by percent_minor_introns descending
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Suggested facets: phylum, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1529436 | Anneissia japonica | Comatulidae | Comatulida | Echinodermata | GCF_011630105.1 | 583 | 155652 | 0.373155822959004 | 92.9 | ["u11", "u12", "u4atac", "u6atac"] | ASM1163010v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/630/105/GCF_011630105.1_ASM1163010v1 | GCF_011630105.1;PRJNA615663;SAMN12241982;VUNX00000000.1;representative genome;1529436;1529436;Anneissia japonica;;Jap-2015-1;latest;Scaffold;Major;Full;2020/03/23;ASM1163010v1;Center for Ecological and Environmental Sciences;GCA_011630105.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/630/105/GCF_011630105.1_ASM1163010v1;;;na | 1 |
| 84834 | Molothrus ater | Icteridae | Passeriformes | Chordata | GCF_012460135.1 | 583 | 164681 | 0.3527689030883919 | 100.0 | ["u11", "u12", "u4atac", "u6atac"] | BPBGC_Mater_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/460/135/GCF_012460135.1_BPBGC_Mater_1.0 | GCF_012460135.1;PRJNA665515;SAMN14074414;JAAQZI000000000.1;representative genome;84834;84834;Molothrus ater;breed=brown headed cowbird;BHLD 08-10-18;latest;Chromosome;Major;Full;2020/04/20;BPBGC_Mater_1.0;Brood Parasitic Bird Genomes Consortium;GCA_012460135.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/460/135/GCF_012460135.1_BPBGC_Mater_1.0;;;na | 1 |
| 146911 | Gekko japonicus | Gekkonidae | Squamata | Chordata | GCF_001447785.1 | 583 | 169307 | 0.3431632232621108 | 92.2 | ["u11", "u12", "u4atac", "u6atac"] | Gekko_japonicus_V1.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/447/785/GCF_001447785.1_Gekko_japonicus_V1.1 | GCF_001447785.1;PRJNA308133;SAMN04157958;LNDG00000000.1;representative genome;146911;146911;Gekko japonicus;;JY-2015;latest;Scaffold;Major;Full;2015/11/25;Gekko_japonicus_V1.1;Nantong University;GCA_001447785.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/447/785/GCF_001447785.1_Gekko_japonicus_V1.1;;;na | 1 |
| 9365 | Erinaceus europaeus | Erinaceidae | Eulipotyphla | Chordata | GCF_000296755.1 | 583 | 172889 | 0.3360772920125438 | 96.1 | ["u11", "u12", "u4atac", "u6atac"] | EriEur2.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/296/755/GCF_000296755.1_EriEur2.0 | GCF_000296755.1;PRJNA232766;SAMN00760989;AMDU00000000.1;representative genome;9365;9365;Erinaceus europaeus;;Erinaceus europaeus_13Jul2011;latest;Scaffold;Major;Full;2012/09/19;EriEur2.0;Broad Institute;GCA_000296755.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/296/755/GCF_000296755.1_EriEur2.0;;;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]);