{ "type": "genome", "identifier": "GCF_000018145.1", "organism": "Dinoroseobacter shibae DFL 12 = DSM 16493", "title": "Dinoroseobacter shibae DFL 12 = DSM 16493", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000018145.1", "bioproject": "PRJNA224116", "biosample": "SAMN02598387", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "398580", "species_taxid": "215813", "organism_name": "Dinoroseobacter shibae DFL 12 = DSM 16493", "infraspecific_name": "strain=DFL 12", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2007/10/05", "asm_name": "ASM1814v1", "asm_submitter": "US DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000018145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/145/GCF_000018145.1_ASM1814v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4417868", "genome_size_ungapped": "4417868", "gc_percent": "65.500000", "replicon_count": "6", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000018145.1-RS_2024_05_01", "annotation_date": "2024-05-01", "total_gene_count": "4329", "protein_coding_gene_count": "4225", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2007-10-05", "dateModified": "2007-10-05", "datePublished": "2007-10-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Dinoroseobacter shibae DFL 12 = DSM 16493" ], "sample_taxid": [ "398580" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.219 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4417868", "Number of Sequences": "6", "Longest Sequences (bp)": "3789584", "N50 (bp)": "3789584", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.5", "Number of CDSs": "4321", "Average Protein Length": "307.7", "Coding Ratio (%)": "90.3", "Number of rRNAs": "6", "Number of tRNAs": "47", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Dinoroseobacter shibae", "strain": "strain=DFL 12", "accession": "GCA_000018145.1", "taxid": 215813, "species_taxid": 215813, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1455, "total_fragments": 1470, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodovulum adriaticum", "strain": "strain=DSM 2781", "accession": "GCA_016583705.1", "taxid": 35804, "species_taxid": 35804, "relation_to_type": "type", "validated": true, "ani": 79.5233, "matched_fragments": 421, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum adriaticum", "strain": "strain=DSM 2781", "accession": "GCA_004345735.1", "taxid": 35804, "species_taxid": 35804, "relation_to_type": "type", "validated": true, "ani": 79.449, "matched_fragments": 425, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevirhabdus pacifica", "strain": "strain=22DY15", "accession": "GCA_002094875.1", "taxid": 1267768, "species_taxid": 1267768, "relation_to_type": "type", "validated": true, "ani": 79.2963, "matched_fragments": 359, 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"status": "below_threshold" }, { "organism_name": "Cribrihabitans marinus", "strain": "strain=DSM 29340", "accession": "GCA_900109035.1", "taxid": 1227549, "species_taxid": 1227549, "relation_to_type": "type", "validated": true, "ani": 78.8169, "matched_fragments": 504, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Antarcticimicrobium luteum", "strain": "strain=318-1", "accession": "GCA_004358185.1", "taxid": 2547397, "species_taxid": 2547397, "relation_to_type": "type", "validated": true, "ani": 78.6831, "matched_fragments": 483, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum robiginosum", "strain": "strain=DSM 12329", "accession": "GCA_003944755.1", "taxid": 68292, "species_taxid": 68292, "relation_to_type": "type", "validated": true, "ani": 78.6825, "matched_fragments": 478, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus isoporae", "strain": "strain=DSM 22220", "accession": "GCA_900101865.1", "taxid": 591205, "species_taxid": 591205, "relation_to_type": "type", "validated": true, "ani": 78.5674, "matched_fragments": 315, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibacterium elongatum", "strain": "strain=DFL-43", "accession": "GCA_000590925.1", "taxid": 159346, "species_taxid": 159346, "relation_to_type": "type", "validated": true, "ani": 78.5549, "matched_fragments": 423, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum tesquicola", "strain": "strain=A-36s", "accession": "GCA_024128855.1", "taxid": 540254, "species_taxid": 540254, "relation_to_type": "type", "validated": true, "ani": 78.5016, "matched_fragments": 459, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum sulfidophilum", "strain": "strain=DSM 1374", "accession": "GCA_001633165.1", "taxid": 35806, "species_taxid": 35806, "relation_to_type": "type", "validated": true, "ani": 78.487, "matched_fragments": 442, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum sulfidophilum", "strain": "strain=DSM 1374", "accession": "GCA_000520135.2", "taxid": 35806, "species_taxid": 35806, "relation_to_type": "type", "validated": true, "ani": 78.4075, "matched_fragments": 451, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum strictum", "strain": "strain=DSM 11289", "accession": "GCA_009649175.1", "taxid": 58314, "species_taxid": 58314, "relation_to_type": "type", "validated": true, "ani": 78.3211, "matched_fragments": 435, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria sediminis", "strain": "strain=CAU 1488", "accession": "GCA_005938215.1", "taxid": 2583820, "species_taxid": 2583820, "relation_to_type": "type", "validated": true, "ani": 78.3101, "matched_fragments": 396, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum visakhapatnamense", "strain": "strain=JA181", "accession": "GCA_004365965.1", "taxid": 364297, "species_taxid": 364297, "relation_to_type": "type", "validated": true, "ani": 78.2937, "matched_fragments": 490, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limimaricola variabilis", "strain": "strain=CECT 8572", "accession": "GCA_014195545.1", "taxid": 1492771, "species_taxid": 1492771, "relation_to_type": "type", "validated": true, "ani": 78.2673, "matched_fragments": 396, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jannaschia formosa", "strain": "strain=12N15", "accession": "GCA_003340555.1", "taxid": 2259592, "species_taxid": 2259592, "relation_to_type": "type", "validated": true, 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1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mangrovicoccus ximenensis", "strain": "strain=T1lg56", "accession": "GCA_003056725.1", "taxid": 1911570, "species_taxid": 1911570, "relation_to_type": "type", "validated": true, "ani": 77.8764, "matched_fragments": 421, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioclava electrotropha", "strain": "strain=Elox9", "accession": "GCA_002085925.2", "taxid": 1549850, "species_taxid": 1549850, "relation_to_type": "type", "validated": true, "ani": 77.7679, "matched_fragments": 372, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aminovorans", "strain": "", "accession": "GCA_900005615.1", "taxid": 34004, "species_taxid": 34004, "relation_to_type": "type", "validated": true, "ani": 77.5943, "matched_fragments": 334, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aminovorans", "strain": "strain=DSM 8537", "accession": "GCA_900113565.1", "taxid": 34004, "species_taxid": 34004, "relation_to_type": "type", "validated": true, "ani": 77.5485, "matched_fragments": 320, "total_fragments": 1470, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000018145.1", "gtdb_species": "s__Dinoroseobacter shibae", "ani": 100.0, "matched_fragments": 1459, "total_fragments": 1470, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCF_002285435.1", "gtdb_species": "s__Actibacterium ureilyticum", 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