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)
4 rows where phylum = "Evosea" sorted by percent_minor_introns descending
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Suggested facets: 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5791 | Physarum polycephalum | Physaraceae | Physariida | Evosea | GCA_000413255.3 | 20295 | 159710 | 11.27468681425516 | 66.3 | ["u11", "u12", "u6atac"] | Physarum_polycephalum-10.0 | ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/413/255/GCA_000413255.3_Physarum_polycephalum-10.0 | GCA_000413255.3;PRJNA12851;SAMN02839457;ATCM00000000.3;representative genome;5791;5791;Physarum polycephalum;strain=LU352;;latest;Scaffold;Major;Full;2014/06/30;Physarum_polycephalum-10.0;WUGSC;na;na;ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/413/255/GCA_000413255.3_Physarum_polycephalum-10.0;;;na | 1 |
| 1890364 | Planoprotostelium fungivorum | Cavosteliaceae | Cavosteliida | Evosea | GCA_003024175.1 | 265 | 139842 | 0.1891411564018928 | 93.7 | ["u11", "u12", "u4atac", "u6atac"] | ASM302417v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/024/175/GCA_003024175.1_ASM302417v1 | GCA_003024175.1;PRJNA338377;SAMN05554249;MDYQ00000000.1;representative genome;1890364;1890364;Planoprotostelium fungivorum;strain=Jena;;latest;Contig;Major;Full;2018/03/12;ASM302417v1;The Protostelium analysis consortium;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/024/175/GCA_003024175.1_ASM302417v1;;;na | 1 |
| 1580589 | Pelomyxa schiedti | Pelomyxidae | Pelobiontida | Evosea | GCA_020536535.1 | 90 | 148036 | 0.0607590834829807 | 80.4 | ["u11", "u12", "u4atac", "u6atac"] | ASM2053653v1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/536/535/GCA_020536535.1_ASM2053653v1 | GCA_020536535.1;PRJNA672820;SAMN16578620;JAHLWZ000000000.1;representative genome;1580589;1580589;Pelomyxa schiedti;strain=SKADARSKE;;latest;Scaffold;Major;Full;2021/10/20;ASM2053653v1;Charles University, BIOCEV;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/536/535/GCA_020536535.1_ASM2053653v1;;;na | 1 |
| 2086695 | Heterostelium album | Acytosteliaceae | Acytosteliales | Evosea | GCF_000004825.1 | 7 | 32736 | 0.0213786152765476 | 86.7 | ["u11", "u4atac", "u6atac"] | PolPal_Dec2009 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/825/GCF_000004825.1_PolPal_Dec2009 | GCF_000004825.1;PRJNA46447;SAMN02953767;ADBJ00000000.1;representative genome;670386;2086695;Heterostelium album PN500;strain=PN500;;latest;Scaffold;Major;Full;2010/01/29;PolPal_Dec2009;Leibniz Institute for Age Research - Fritz Lipmann Institute;GCA_000004825.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/825/GCF_000004825.1_PolPal_Dec2009;;;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]);