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)
6 rows where phylum = "Zoopagomycota" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
Suggested facets: family, order, minor_snRNAs, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 423460 | Basidiobolus meristosporus | Basidiobolaceae | Basidiobolales | Zoopagomycota | GCA_002104905.1 | 249 | 44710 | 0.5538379412353477 | 96.5 | ["u11", "u12", "u4atac", "u6atac"] | Basme2finSC | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/905/GCA_002104905.1_Basme2finSC | GCA_002104905.1;PRJNA196075;SAMN02745972;MCFE00000000.1;representative genome;1314790;423460;Basidiobolus meristosporus CBS 931.73;strain=CBS 931.73;;latest;Contig;Major;Full;2017/04/20;Basme2finSC;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/905/GCA_002104905.1_Basme2finSC;;;na | 1 |
| 78915 | Thamnocephalis sphaerospora | Sigmoideomycetaceae | Zoopagales | Zoopagomycota | GCA_003614735.1 | 67 | 25406 | 0.2630235936089192 | 78.0 | ["u11", "u4atac", "u6atac"] | Thasp1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/614/735/GCA_003614735.1_Thasp1 | GCA_003614735.1;PRJNA421763;SAMN09741940;QUVU00000000.1;representative genome;78915;78915;Thamnocephalis sphaerospora;strain=RSA 1356;;latest;Scaffold;Major;Full;2018/10/04;Thasp1;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/614/735/GCA_003614735.1_Thasp1;derived from single cell;;na | 1 |
| 1712513 | Syncephalis pseudoplumigaleata | Piptocephalidaceae | Zoopagales | Zoopagomycota | GCA_003614755.1 | 41 | 19102 | 0.2141775061380139 | 57.6 | ["u11", "u12", "u4atac", "u6atac"] | Synps1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/614/755/GCA_003614755.1_Synps1 | GCA_003614755.1;PRJNA421590;SAMN09741936;QUVV00000000.1;representative genome;1712513;1712513;Syncephalis pseudoplumigaleata;strain=Benny S71-1;;latest;Scaffold;Major;Full;2018/10/04;Synps1;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/614/755/GCA_003614755.1_Synps1;derived from single cell;;na | 1 |
| 42810 | Entomophaga maimaiga | Entomophthoraceae | Entomophthorales | Zoopagomycota | Entmai1 | 40 | 32976 | 0.1211533801793069 | 93.3 | ["u11", "u12", "u4atac", "u6atac"] | . | . | 1 | |
| 34485 | Entomophthora muscae | Entomophthoraceae | Entomophthorales | Zoopagomycota | GCA_014839935.1 | 23 | 46567 | 0.0493668169135007 | 78.4 | ["u11", "u12", "u4atac", "u6atac"] | Emusc_Berkeley_10X_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/839/935/GCA_014839935.1_Emusc_Berkeley_10X_1.0 | GCA_014839935.1;PRJNA479887;SAMN09621101;QTSX00000000.1;representative genome;34485;34485;Entomophthora muscae;strain=Berkeley;;latest;Scaffold;Major;Full;2020/10/02;Emusc_Berkeley_10X_1.0;University of California, Berkeley;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/839/935/GCA_014839935.1_Emusc_Berkeley_10X_1.0;;;na | 1 |
| 34488 | Conidiobolus coronatus | Ancylistaceae | Entomophthorales | Zoopagomycota | GCA_001566745.1 | 9 | 18300 | 0.049156152711781 | 80.0 | ["u11", "u12", "u4atac", "u6atac"] | Conidiobolus coronatus NRRL28638 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/566/745/GCA_001566745.1_Conidiobolus_coronatus_NRRL28638 | GCA_001566745.1;PRJNA67455;SAMN00779232;JXYT00000000.1;representative genome;796925;34488;Conidiobolus coronatus NRRL 28638;strain=NRRL 28638;;latest;Scaffold;Major;Full;2016/02/24;Conidiobolus coronatus NRRL28638;JGI-PSF;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/566/745/GCA_001566745.1_Conidiobolus_coronatus_NRRL28638;;;na | 1 |
Advanced export
JSON shape: default, array, newline-delimited, object
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]);