{ "type": "genome", "identifier": "GCF_031453995.1", "organism": "Nitrobacter vulgaris", "title": "Nitrobacter vulgaris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_031453995.1", "bioproject": "PRJNA224116", "biosample": "SAMN13172834", "wgs_master": "JAVDPZ000000000.1", "refseq_category": "reference genome", "taxid": "29421", "species_taxid": "29421", "organism_name": "Nitrobacter vulgaris", "infraspecific_name": "strain=DSM 10236", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/09/13", "asm_name": "ASM3145399v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_031453995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/031/453/995/GCF_031453995.1_ASM3145399v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4293395", "genome_size_ungapped": "4293395", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "98", "contig_count": "98", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_031453995.1-RS_2024_09_15", "annotation_date": "2024-09-15", "total_gene_count": "4172", "protein_coding_gene_count": "3917", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-09-13", "dateModified": "2023-09-13", "datePublished": "2023-09-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrobacter vulgaris" ], "sample_taxid": [ "29421" ], "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": "1.219 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)": "4293395", "Number of Sequences": "98", "Longest Sequences (bp)": "226412", "N50 (bp)": "110847", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.5", "Number of CDSs": "4143", "Average Protein Length": "270.7", "Coding Ratio (%)": "78.4", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nitrobacter winogradskyi", "strain": "strain=Nb-255", "accession": "GCA_000012725.1", "taxid": 913, "species_taxid": 913, "relation_to_type": "type", "validated": true, "ani": 86.5926, "matched_fragments": 857, "total_fragments": 1379, "ani_threshold": 95, 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"GCA_020889685.1", "taxid": 1571201, "species_taxid": 1571201, "relation_to_type": "type", "validated": true, "ani": 78.7805, "matched_fragments": 452, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium murdochi", "strain": "strain=WSM 1741", "accession": "GCA_000472965.1", "taxid": 1038859, "species_taxid": 1038859, "relation_to_type": "type", "validated": true, "ani": 78.7773, "matched_fragments": 482, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium acaciae", "strain": "strain=10BB", "accession": "GCA_020889785.1", "taxid": 2683706, "species_taxid": 2683706, "relation_to_type": "type", "validated": true, "ani": 78.7517, "matched_fragments": 460, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cajani", "strain": "strain=1010", "accession": "GCA_009759665.1", "taxid": 1928661, "species_taxid": 1928661, "relation_to_type": "type", "validated": true, "ani": 78.728, "matched_fragments": 449, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium lablabi", "strain": "strain=CCBAU 23086", "accession": "GCA_001440475.1", "taxid": 722472, "species_taxid": 722472, "relation_to_type": "suspected-type", "validated": true, "ani": 78.7143, "matched_fragments": 503, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium huanghuaihaiense", "strain": "strain=CGMCC 1.10948", "accession": "GCA_007830635.1", "taxid": 990078, "species_taxid": 990078, "relation_to_type": "type", "validated": true, "ani": 78.7024, "matched_fragments": 470, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium valentinum", "strain": "strain=LmjM3", "accession": "GCA_001440405.1", "taxid": 1518501, "species_taxid": 1518501, "relation_to_type": "type", "validated": true, "ani": 78.6843, "matched_fragments": 493, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium frederickii", "strain": "strain=CNPSo 3426", "accession": "GCA_004570865.1", "taxid": 2560054, "species_taxid": 2560054, "relation_to_type": "type", "validated": true, "ani": 78.6341, "matched_fragments": 439, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cytisi", "strain": "strain=CTAW11", "accession": "GCA_008123515.1", "taxid": 515489, "species_taxid": 515489, "relation_to_type": "type", "validated": true, "ani": 78.6328, "matched_fragments": 434, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diversitatis", "strain": "strain=CNPSo 4019", "accession": "GCA_016031635.1", "taxid": 2755406, "species_taxid": 2755406, "relation_to_type": "type", "validated": true, "ani": 78.6298, "matched_fragments": 462, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium nitroreducens", "strain": "strain=TSA1", "accession": "GCA_002776695.1", "taxid": 709803, "species_taxid": 709803, "relation_to_type": "type", "validated": true, "ani": 78.4575, "matched_fragments": 464, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium betae", "strain": "strain=CECT 5829", "accession": "GCA_024806875.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 78.4566, "matched_fragments": 450, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002028545.1", "gtdb_species": "s__Nitrobacter vulgaris", "ani": 98.2895, "matched_fragments": 1080, "total_fragments": 1379, 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"d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Nitrobacter", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.039, "doubling_h": 1.206, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 4206807.0, "gc_content": 61.65, "coding_genes": 3746.833, "rRNA16S_genes": 1.0, "tRNA_genes": 52.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.5, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.5, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 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