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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

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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

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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]);
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