{ "type": "genome", "identifier": "GCF_003053725.1", "organism": "Rhodovulum kholense", "title": "Rhodovulum kholense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003053725.1", "bioproject": "PRJNA224116", "biosample": "SAMN08779096", "wgs_master": "QAYC00000000.1", "refseq_category": "reference genome", "taxid": "453584", "species_taxid": "453584", "organism_name": "Rhodovulum kholense", "infraspecific_name": "strain=DSM 19783", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/17", "asm_name": "ASM305372v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003053725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/053/725/GCF_003053725.1_ASM305372v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4458411", "genome_size_ungapped": "4458411", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "51", "contig_count": "51", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003053725.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "4264", "protein_coding_gene_count": "4134", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-17", "dateModified": "2018-04-17", "datePublished": "2018-04-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodovulum kholense" ], "sample_taxid": [ "453584" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.212 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4458411", "Number of Sequences": "51", "Longest Sequences (bp)": "605830", "N50 (bp)": "229701", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.8", "Number of CDSs": "4230", "Average Protein Length": "313.5", "Coding Ratio (%)": "89.2", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodovulum visakhapatnamense", "strain": "strain=JA181", "accession": "GCA_004365965.1", "taxid": 364297, "species_taxid": 364297, "relation_to_type": "type", "validated": true, "ani": 94.3562, "matched_fragments": 1242, "total_fragments": 1457, "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": 88.5298, "matched_fragments": 1079, "total_fragments": 1457, "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": 88.4181, "matched_fragments": 1101, "total_fragments": 1457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum euryhalinum", "strain": "strain=DSM 4868", "accession": "GCA_004342445.1", "taxid": 35805, "species_taxid": 35805, "relation_to_type": "type", "validated": true, "ani": 82.0463, "matched_fragments": 803, "total_fragments": 1457, "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": 82.0417, "matched_fragments": 735, "total_fragments": 1457, "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": 82.0367, "matched_fragments": 744, "total_fragments": 1457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum marinum", "strain": "strain=DSM 18063", "accession": "GCA_004343075.1", "taxid": 320662, "species_taxid": 320662, "relation_to_type": "type", "validated": true, "ani": 81.6784, "matched_fragments": 804, "total_fragments": 1457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum adriaticum", "strain": "strain=DSM 2781", "accession": "GCA_016583705.1", "taxid": 35804, "species_taxid": 35804, "relation_to_type": "type", "validated": true, "ani": 80.7501, "matched_fragments": 631, "total_fragments": 1457, "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": 80.7468, "matched_fragments": 642, "total_fragments": 1457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter johrii", "strain": "strain=JA192", "accession": "GCA_003046325.1", "taxid": 445629, "species_taxid": 445629, "relation_to_type": "type", "validated": true, "ani": 79.0485, "matched_fragments": 585, "total_fragments": 1457, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Palleronia sediminis", "strain": "strain=SS33", "accession": "GCA_004358695.1", "taxid": 2547833, "species_taxid": 2547833, 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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": "-" }, { "accession": "GCF_004343075.1", "gtdb_species": "s__Rhodovulum marinum", "ani": 81.6896, "matched_fragments": 803, "total_fragments": 1457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum", "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": "-" }, { "accession": "GCF_004345735.1", "gtdb_species": "s__Rhodovulum adriaticum", "ani": 80.7528, "matched_fragments": 641, "total_fragments": 1457, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": 7.628, "genome_size": 4458411.0, "gc_content": 67.433, "coding_genes": 4097.399, "rRNA16S_genes": 3.0, "tRNA_genes": 50.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.3, "anaerobic_respiration": 0.4, "aerobic_respiration": 0.3, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhodovulum", "kholense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }