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)
11 rows where phylum = "Nematoda" sorted by percent_minor_introns descending
This data as json, CSV (advanced)
Suggested facets: family, n_minor_introns, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 181606 | Trichinella sp. t9 | Trichinellidae | Trichinellida | Nematoda | GCA_001447505.1 | 11 | 69585 | 0.0158055060635668 | 80.4 | ["u11", "u12", "u4atac", "u6atac"] | T9_ISS409_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/505/GCA_001447505.1_T9_ISS409_r1.0 | GCA_001447505.1;PRJNA257433;SAMN02949488;JYDN00000000.1;representative genome;181606;181606;Trichinella sp. T9;;ISS409;latest;Scaffold;Major;Full;2015/11/24;T9_ISS409_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/505/GCA_001447505.1_T9_ISS409_r1.0;;;na | 1 |
| 990121 | Trichinella patagoniensis | Trichinellidae | Trichinellida | Nematoda | GCA_001447655.1 | 8 | 71956 | 0.011116669445834 | 83.9 | ["u11", "u12", "u4atac", "u6atac"] | T12_ISS2496_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/655/GCA_001447655.1_T12_ISS2496_r1.0 | GCA_001447655.1;PRJNA257433;SAMN02949507;JYDQ00000000.1;representative genome;990121;990121;Trichinella patagoniensis;;ISS2496;latest;Scaffold;Major;Full;2015/11/24;T12_ISS2496_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/655/GCA_001447655.1_T12_ISS2496_r1.0;;;na | 1 |
| 268474 | Trichinella papuae | Trichinellidae | Trichinellida | Nematoda | GCA_001447755.1 | 7 | 67404 | 0.0103840619483467 | 82.7 | ["u11", "u12", "u4atac", "u6atac"] | T10_ISS1980_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/755/GCA_001447755.1_T10_ISS1980_r1.0 | GCA_001447755.1;PRJNA257433;SAMN02949504;JYDO00000000.1;representative genome;268474;268474;Trichinella papuae;;ISS1980;latest;Scaffold;Major;Full;2015/11/24;T10_ISS1980_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/755/GCA_001447755.1_T10_ISS1980_r1.0;;;na | 1 |
| 6337 | Trichinella pseudospiralis | Trichinellidae | Trichinellida | Nematoda | GCA_001447645.1 | 7 | 67692 | 0.0103398868520953 | 77.6 | ["u11", "u12", "u4atac", "u6atac"] | T4_ISS176_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/645/GCA_001447645.1_T4_ISS176_r1.0 | GCA_001447645.1;PRJNA257433;SAMN02949477;JYDV00000000.1;representative genome;6337;6337;Trichinella pseudospiralis;;ISS176 (KAZ);latest;Scaffold;Major;Full;2015/11/24;T4_ISS176_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/645/GCA_001447645.1_T4_ISS176_r1.0;;;na | 1 |
| 268475 | Trichinella zimbabwensis | Trichinellidae | Trichinellida | Nematoda | GCA_001447665.1 | 6 | 69811 | 0.0085938954695847 | 82.0 | ["u11", "u12", "u4atac", "u6atac"] | T11_ISS1029_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/665/GCA_001447665.1_T11_ISS1029_r1.0 | GCA_001447665.1;PRJNA257433;SAMN02949506;JYDP00000000.1;representative genome;268475;268475;Trichinella zimbabwensis;;ISS1029;latest;Scaffold;Major;Full;2015/11/24;T11_ISS1029_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/665/GCA_001447665.1_T11_ISS1029_r1.0;;;na | 1 |
| 68888 | Trichuris suis | Trichuridae | Trichinellida | Nematoda | GCA_000797535.1 | 4 | 51668 | 0.0077411363988233 | 83.5 | ["u11", "u12", "u4atac", "u6atac"] | T_suis_1.0.allpaths | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/797/535/GCA_000797535.1_T_suis_1.0.allpaths | GCA_000797535.1;PRJNA179528;SAMN02721381;JDFW00000000.1;representative genome;68888;68888;Trichuris suis;;;latest;Scaffold;Major;Full;2014/12/09;T_suis_1.0.allpaths;The Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/797/535/GCA_000797535.1_T_suis_1.0.allpaths;;;na | 1 |
| 6334 | Trichinella spiralis | Trichinellidae | Trichinellida | Nematoda | GCF_000181795.1 | 5 | 68661 | 0.0072816240934378 | 74.5 | ["u11", "u12", "u4atac", "u6atac"] | Trichinella spiralis-3.7.1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/181/795/GCF_000181795.1_Trichinella_spiralis-3.7.1 | GCF_000181795.1;PRJNA66457;SAMN02953711;ABIR00000000.2;representative genome;6334;6334;Trichinella spiralis;strain=ISS 195;;latest;Scaffold;Major;Full;2011/01/11;Trichinella spiralis-3.7.1;Washington University School of Medicine;GCA_000181795.2;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/181/795/GCF_000181795.1_Trichinella_spiralis-3.7.1;;;na | 1 |
| 6336 | Trichinella nelsoni | Trichinellidae | Trichinellida | Nematoda | GCA_001447455.1 | 5 | 69896 | 0.0071529734910802 | 87.5 | ["u11", "u12", "u4atac", "u6atac"] | T7_ISS37_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/455/GCA_001447455.1_T7_ISS37_r1.0 | GCA_001447455.1;PRJNA257433;SAMN02949482;JYDL00000000.1;representative genome;6336;6336;Trichinella nelsoni;;ISS37;latest;Scaffold;Major;Full;2015/11/24;T7_ISS37_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/455/GCA_001447455.1_T7_ISS37_r1.0;;;na | 1 |
| 45882 | Trichinella britovi | Trichinellidae | Trichinellida | Nematoda | GCA_001447585.1 | 5 | 72637 | 0.006883070400044 | 86.3 | ["u11", "u12", "u4atac", "u6atac"] | T3_ISS120_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/585/GCA_001447585.1_T3_ISS120_r1.0 | GCA_001447585.1;PRJNA257433;SAMN02949469;JYDI00000000.1;representative genome;45882;45882;Trichinella britovi;;ISS120;latest;Scaffold;Major;Full;2015/11/24;T3_ISS120_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/585/GCA_001447585.1_T3_ISS120_r1.0;;;na | 1 |
| 6335 | Trichinella nativa | Trichinellidae | Trichinellida | Nematoda | GCA_001447565.1 | 4 | 71019 | 0.005631978373203 | 89.4 | ["u11", "u12", "u4atac", "u6atac"] | T2_ISS10_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/565/GCA_001447565.1_T2_ISS10_r1.0 | GCA_001447565.1;PRJNA257433;SAMN02949468;JYDW00000000.1;representative genome;6335;6335;Trichinella nativa;;ISS10;latest;Scaffold;Major;Full;2015/11/24;T2_ISS10_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/565/GCA_001447565.1_T2_ISS10_r1.0;;;na | 1 |
| 92180 | Trichinella sp. t8 | Trichinellidae | Trichinellida | Nematoda | GCA_001447745.1 | 3 | 72294 | 0.0041495497738495 | 89.0 | ["u11", "u12", "u4atac", "u6atac"] | T8_ISS272_r1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/745/GCA_001447745.1_T8_ISS272_r1.0 | GCA_001447745.1;PRJNA257433;SAMN02949483;JYDM00000000.1;representative genome;92180;92180;Trichinella sp. T8;;ISS272;latest;Scaffold;Major;Full;2015/11/24;T8_ISS272_r1.0;University of Melbourne;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/447/745/GCA_001447745.1_T8_ISS272_r1.0;;;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]);