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)
6 rows where family = "Passeridae" and minor_snRNAs contains "u12" sorted by percent_minor_introns descending
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Suggested facets: 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 356909 | Onychostruthus taczanowskii | Passeridae | Passeriformes | Chordata | GCF_017590055.1 | 568 | 158940 | 0.3560949921007096 | 98.4 | ["u11", "u12", "u4atac", "u6atac"] | ASM1759005v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/590/055/GCF_017590055.1_ASM1759005v1 | GCF_017590055.1;PRJNA703052;SAMN18252883;JAGGNI000000000.1;representative genome;356909;356909;Onychostruthus taczanowskii;;IOZ18803;latest;Scaffold;Major;Full;2021/03/26;ASM1759005v1;Institute of Zoology, Chinese Academy of Sciences;GCA_017590055.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/590/055/GCF_017590055.1_ASM1759005v1;;;na | 1 |
| 221976 | Pyrgilauda ruficollis | Passeridae | Passeriformes | Chordata | GCF_017590135.1 | 563 | 158977 | 0.3528895574777485 | 96.5 | ["u11", "u12", "u4atac", "u6atac"] | ASM1759013v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/590/135/GCF_017590135.1_ASM1759013v1 | GCF_017590135.1;PRJNA703052;SAMN18252884;JAGGNJ000000000.1;representative genome;221976;221976;Pyrgilauda ruficollis;;IOZ18807;latest;Scaffold;Major;Full;2021/03/26;ASM1759013v1;Institute of Zoology, Chinese Academy of Sciences;GCA_017590135.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/590/135/GCF_017590135.1_ASM1759013v1;;;na | 1 |
| 9160 | Passer montanus | Passeridae | Passeriformes | Chordata | GCF_014805655.1 | 570 | 164616 | 0.3450655624568668 | 96.9 | ["u11", "u12", "u4atac", "u6atac"] | ASM1480565v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/805/655/GCF_014805655.1_ASM1480565v1 | GCF_014805655.1;PRJNA703052;SAMN07998528;JABBVY000000000.1;representative genome;9160;9160;Passer montanus;;IOZ18808;latest;Scaffold;Major;Full;2020/09/30;ASM1480565v1;Institute of Zoology, Chinese Academy of Sciences;GCA_014805655.1;different;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/805/655/GCF_014805655.1_ASM1480565v1;;;na | 1 |
| 670355 | Prunella fulvescens | Passeridae | Passeriformes | Chordata | GCA_013400715.1 | 256 | 89512 | 0.2851795740130113 | 76.5 | ["u11", "u12", "u4atac", "u6atac"] | ASM1340071v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/400/715/GCA_013400715.1_ASM1340071v1 | GCA_013400715.1;PRJNA545868;SAMN12253912;VZTP00000000.1;representative genome;670355;670355;Prunella fulvescens;;B10K-DU-012-46;latest;Scaffold;Major;Full;2020/07/10;ASM1340071v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/400/715/GCA_013400715.1_ASM1340071v1;;;na | 1 |
| 670356 | Prunella himalayana | Passeridae | Passeriformes | Chordata | GCA_013398875.1 | 290 | 105403 | 0.2743795710217327 | 84.7 | ["u11", "u12", "u4atac", "u6atac"] | ASM1339887v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/875/GCA_013398875.1_ASM1339887v1 | GCA_013398875.1;PRJNA545868;SAMN12253920;VYZK00000000.1;representative genome;670356;670356;Prunella himalayana;;B10K-DU-013-18;latest;Scaffold;Major;Full;2020/07/10;ASM1339887v1;B10K Consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/398/875/GCA_013398875.1_ASM1339887v1;;;na | 1 |
| 44316 | Chloebia gouldiae | Passeridae | Passeriformes | Chordata | GCA_003676055.1 | 271 | 142657 | 0.1896059554460987 | 80.0 | ["u11", "u12", "u4atac", "u6atac"] | GouldianFinch | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/676/055/GCA_003676055.1_GouldianFinch | GCA_003676055.1;PRJNA478907;SAMN09689584;QUSF00000000.1;representative genome;44316;44316;Chloebia gouldiae;;Red01;latest;Scaffold;Major;Full;2018/10/23;GouldianFinch;CIBIO/InBIO Research Center in Biodiversity and Genetic Resources;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/676/055/GCA_003676055.1_GouldianFinch;;;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]);