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 = "Annelida" sorted by percent_minor_introns descending
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Suggested facets: order, 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+ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 104711 | Lamellibrachia satsuma | Siboglinidae | Sabellida | Annelida | GCA_022478865.1 | 526 | 176978 | 0.2963313502794303 | 90.6 | ["u11", "u12", "u4atac", "u6atac"] | MABIK_Lsat_1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/478/865/GCA_022478865.1_MABIK_Lsat_1.0 | GCA_022478865.1;PRJNA736170;SAMN19689423;JAHXPS000000000.1;representative genome;104711;104711;Lamellibrachia satsuma;;1372_Tw2;latest;Contig;Major;Full;2022/03/04;MABIK_Lsat_1.0;National Marine Biodiversity Institute of Korea;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/478/865/GCA_022478865.1_MABIK_Lsat_1.0;;;na | 1 |
| 6347 | Owenia fusiformis | Oweniidae | Sabellida | Annelida | GCA_903813345.2 | 492 | 167123 | 0.2935298153506547 | 97.3 | ["u11", "u12", "u4atac", "u6atac"] | Owenia_chromosome | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/813/345/GCA_903813345.2_Owenia_chromosome | GCA_903813345.2;PRJEB38497;SAMEA6870334;CAIIXF000000000.2;representative genome;6347;6347;Owenia fusiformis;;;latest;Scaffold;Major;Full;2022/03/14;Owenia_chromosome;QUEEN MARY UNIVERSITY OF LONDON;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/813/345/GCA_903813345.2_Owenia_chromosome;;;na | 1 |
| 95538 | Streblospio benedicti | Spionidae | Spionida | Annelida | GCA_019095985.1 | 145 | 54786 | 0.2639675228923558 | 55.7 | ["u11", "u12", "u4atac", "u6atac"] | ASM1909598v1 | ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/095/985/GCA_019095985.1_ASM1909598v1 | GCA_019095985.1;PRJNA721660;SAMN18729079;JAGTTF000000000.1;representative genome;95538;95538;Streblospio benedicti;;BayGN2011;latest;Chromosome;Major;Full;2021/07/06;ASM1909598v1;North Carolina State University;na;na;ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/095/985/GCA_019095985.1_ASM1909598v1;;;na | 1 |
| 283909 | Capitella teleta | Capitellidae | Annelida | GCA_000328365.1 | 301 | 139907 | 0.2146810453041196 | 93.3 | ["u11", "u12", "u4atac", "u6atac"] | Capca1 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/328/365/GCA_000328365.1_Capca1 | GCA_000328365.1;PRJNA175705;SAMN02769627;AMQN00000000.1;representative genome;283909;283909;Capitella teleta;strain=I ESC-2004;;latest;Scaffold;Major;Full;2013/01/25;Capca1;DOE Joint Genome Institute;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/328/365/GCA_000328365.1_Capca1;;;na | 1 | |
| 2664684 | Dimorphilus gyrociliatus | Dinophilidae | Annelida | GCA_904063045.1 | 41 | 73111 | 0.0560476815398075 | 96.1 | ["u11", "u12", "u4atac", "u6atac"] | Dgyrociliatus_assembly | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/063/045/GCA_904063045.1_Dgyrociliatus_assembly | GCA_904063045.1;PRJEB37657;SAMEA7202578;CAJFCJ000000000.1;representative genome;2664684;2664684;Dimorphilus gyrociliatus;;;latest;Scaffold;Major;Full;2020/08/25;Dgyrociliatus_assembly;UNIVERSITY OF BERGEN/DEPT. OF BIOLOGY;na;na;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/063/045/GCA_904063045.1_Dgyrociliatus_assembly;;;na | 1 | |
| 6412 | Helobdella robusta | Glossiphoniidae | Rhynchobdellida | Annelida | GCF_000326865.1 | 65 | 118758 | 0.0547032140242209 | 96.9 | ["u11", "u12", "u4atac", "u6atac"] | Helobdella robusta v1.0 | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/326/865/GCF_000326865.1_Helobdella_robusta_v1.0 | GCF_000326865.1;PRJNA259764;SAMN02769625;AMQM00000000.1;representative genome;6412;6412;Helobdella robusta;;;latest;Scaffold;Major;Full;2012/12/20;Helobdella robusta v1.0;DOE Joint Genome Institute;GCA_000326865.1;identical;https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/326/865/GCF_000326865.1_Helobdella_robusta_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]);