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 = "Chytridiomycota" 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1754191 | Piromyces finnis | Neocallimastigaceae | Neocallimastigales | Chytridiomycota | GCA_002104945.1 | 147 | 43177 | 0.3393038500600129 | 88.2 | ["u12", "u4atac", "u6atac"] | Piromyces sp. finnis v3.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/945/GCA_002104945.1_Piromyces_sp._finnis_v3.0 | GCA_002104945.1;PRJNA330696;SAMN05421903;MCFH00000000.1;representative genome;1754191;1754191;Piromyces finnis;strain=finn;;latest;Contig;Major;Full;2017/04/20;Piromyces sp. finnis v3.0;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/945/GCA_002104945.1_Piromyces_sp._finnis_v3.0;;assembly from type material;na | 1 |
| 1754190 | Neocallimastix californiae | Neocallimastigaceae | Neocallimastigales | Chytridiomycota | GCA_002104975.1 | 183 | 65380 | 0.2791208455988896 | 88.6 | ["u12", "u4atac", "u6atac"] | Neocallimastix sp. G1 v1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/975/GCA_002104975.1_Neocallimastix_sp._G1_v1.0 | GCA_002104975.1;PRJNA262392;SAMN05428678;MCOG00000000.1;representative genome;1754190;1754190;Neocallimastix californiae;strain=G1;;latest;Contig;Major;Full;2017/04/20;Neocallimastix sp. G1 v1.0;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/975/GCA_002104975.1_Neocallimastix_sp._G1_v1.0;;assembly from type material;na | 1 |
| 1754192 | Anaeromyces robustus | Neocallimastigaceae | Neocallimastigales | Chytridiomycota | GCA_002104895.1 | 126 | 46705 | 0.269052550660887 | 84.3 | ["u12", "u4atac", "u6atac"] | Anaeromyces sp. S4 v1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/895/GCA_002104895.1_Anaeromyces_sp._S4_v1.0 | GCA_002104895.1;PRJNA330692;SAMN05421914;MCFG00000000.1;representative genome;1754192;1754192;Anaeromyces robustus;strain=S4;;latest;Contig;Major;Full;2017/04/20;Anaeromyces sp. S4 v1.0;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/104/895/GCA_002104895.1_Anaeromyces_sp._S4_v1.0;;assembly from type material;na | 1 |
| 2767002 | Neocallimastix sp. jgi-2020a | Neocallimastigaceae | Neocallimastigales | Chytridiomycota | GCA_016946835.1 | 192 | 98056 | 0.1954238254213826 | 89.8 | ["u12", "u4atac", "u6atac"] | ASM1694683v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/946/835/GCA_016946835.1_ASM1694683v1 | GCA_016946835.1;PRJNA658393;SAMN15902602;JACVTC000000000.1;representative genome;2767002;2767002;Neocallimastix sp. JGI-2020a;strain=sp3;;latest;Contig;Major;Full;2021/02/24;ASM1694683v1;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/946/835/GCA_016946835.1_ASM1694683v1;;;na | 1 |
| 109760 | Spizellomyces punctatus | Spizellomycetaceae | Spizellomycetales | Chytridiomycota | GCF_000182565.1 | 28 | 44281 | 0.0631925793856778 | 94.1 | ["u11", "u12", "u6atac"] | S_punctatus_V1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/182/565/GCF_000182565.1_S_punctatus_V1 | GCF_000182565.1;PRJNA319336;SAMN00716787;ACOE00000000.1;representative genome;645134;109760;Spizellomyces punctatus DAOM BR117;strain=DAOM BR117;;latest;Scaffold;Major;Full;2015/07/29;S_punctatus_V1;Broad Institute;GCA_000182565.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/182/565/GCF_000182565.1_S_punctatus_V1;;;na | 1 |
| 109871 | Batrachochytrium dendrobatidis | Rhizophydiales | Chytridiomycota | GCF_000203795.1 | 3 | 28469 | 0.0105366676032593 | 92.5 | ["u11", "u6atac"] | v1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/203/795/GCF_000203795.1_v1.0 | GCF_000203795.1;PRJNA225502;SAMN02746048;ADAR00000000.1;representative genome;684364;109871;Batrachochytrium dendrobatidis JAM81;strain=JAM81;;latest;Scaffold;Major;Full;2011/04/12;v1.0;US DOE Joint Genome Institute (JGI-PGF);GCA_000203795.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/203/795/GCF_000203795.1_v1.0;;;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]);