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)
3 rows where family = "Branchiostomidae" and minor_snRNAs contains "u11" sorted by percent_minor_introns descending
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Suggested facets: 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 7741 | Branchiostoma belcheri | Branchiostomidae | Amphioxiformes | Chordata | GCF_001625305.1 | 557 | 211490 | 0.2626776139252147 | 99.6 | ["u11", "u12", "u4atac", "u6atac"] | Haploidv18h27 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/625/305/GCF_001625305.1_Haploidv18h27 | GCF_001625305.1;PRJNA358734;SAMN04869859;AYSS00000000.1;representative genome;7741;7741;Branchiostoma belcheri;breed=outbred;BF01;latest;Scaffold;Major;Full;2016/04/21;Haploidv18h27;Sun Yat-sen University;GCA_001625305.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/625/305/GCF_001625305.1_Haploidv18h27;;;na | 1 |
| 7739 | Branchiostoma floridae | Branchiostomidae | Amphioxiformes | Chordata | GCF_000003815.2 | 548 | 214045 | 0.2553671368590774 | 95.7 | ["u11", "u12", "u4atac", "u6atac"] | Bfl_VNyyK | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/815/GCF_000003815.2_Bfl_VNyyK | GCF_000003815.2;PRJNA33245;SAMN02953694;ABEP00000000.3;representative genome;7739;7739;Branchiostoma floridae;strain=S238N-H82;;latest;Chromosome;Major;Full;2020/04/29;Bfl_VNyyK;DOE Joint Genome Institute;GCA_000003815.2;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/815/GCF_000003815.2_Bfl_VNyyK;;;na | 1 |
| 7740 | Branchiostoma lanceolatum | Branchiostomidae | Amphioxiformes | Chordata | GCA_927797965.1 | 508 | 217436 | 0.2330873985978049 | 95.7 | ["u11", "u12", "u4atac", "u6atac"] | BraLan3 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/927/797/965/GCA_927797965.1_BraLan3 | GCA_927797965.1;PRJEB49647;SAMEA11998880;CAKMNS000000000.1;representative genome;7740;7740;Branchiostoma lanceolatum;;;latest;Chromosome;Major;Full;2022/02/02;BraLan3;lausanne university;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/927/797/965/GCA_927797965.1_BraLan3;;;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]);