{ "type": "genome", "identifier": "GCF_002310495.1", "organism": "Nibricoccus aquaticus", "title": "Nibricoccus aquaticus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Nakdonggang National Institute of Biological Resources", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002310495.1", "bioproject": "PRJNA224116", "biosample": "SAMN07628394", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2576891", "species_taxid": "2576891", "organism_name": "Nibricoccus aquaticus", "infraspecific_name": "strain=HZ-65", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/09/18", "asm_name": "ASM231049v1", "asm_submitter": "Nakdonggang National Institute of Biological Resources", "gbrs_paired_asm": "GCA_002310495.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/310/495/GCF_002310495.1_ASM231049v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4730447", "genome_size_ungapped": "4730447", "gc_percent": "62.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002310495.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "3833", "protein_coding_gene_count": "3772", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-09-18", "dateModified": "2017-09-18", "datePublished": "2017-09-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Nibricoccus aquaticus" ], "sample_taxid": [ "2576891" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Chilgok-gun, Gyeongsangbuk-do" ], "sample_host_location_id": [], "data_size": "1.302 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)": "4730447", "Number of Sequences": "1", "Longest Sequences (bp)": "4730447", "N50 (bp)": "4730447", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.2", "Number of CDSs": "3804", "Average Protein Length": "371.8", "Coding Ratio (%)": "89.7", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nibricoccus aquaticus", "strain": "strain=HZ-65", "accession": "GCA_002310495.1", "taxid": 2576891, "species_taxid": 2576891, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1576, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rariglobus hedericola", "strain": "strain=53C-WASEF", "accession": "GCA_007559335.1", "taxid": 2597822, "species_taxid": 2597822, "relation_to_type": "type", "validated": true, "ani": 78.6271, "matched_fragments": 343, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Geminisphaera colitermitum", "strain": "strain=TAV2", "accession": "GCA_000171235.2", "taxid": 1148786, "species_taxid": 1148786, "relation_to_type": "type", "validated": true, "ani": 77.9357, "matched_fragments": 259, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ereboglobus luteus", "strain": "strain=Ho45", "accession": "GCA_003096195.1", "taxid": 1796921, "species_taxid": 1796921, "relation_to_type": "type", "validated": true, "ani": 77.5323, "matched_fragments": 221, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cephaloticoccus primus", "strain": "strain=CAG34", "accession": "GCA_001580015.1", "taxid": 1548207, "species_taxid": 1548207, "relation_to_type": "type", "validated": true, "ani": 77.4043, "matched_fragments": 143, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Opitutus terrae", "strain": "strain=PB90-1", "accession": "GCA_000019965.1", "taxid": 107709, "species_taxid": 107709, "relation_to_type": "type", "validated": true, "ani": 76.891, "matched_fragments": 254, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagicoccus enzymogenes", "strain": "strain=NFK12", "accession": "GCA_014803405.1", "taxid": 2773457, "species_taxid": 2773457, "relation_to_type": "type", "validated": true, "ani": 75.9186, "matched_fragments": 106, "total_fragments": 1576, "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": 75.2418, "matched_fragments": 70, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002310495.1", "gtdb_species": "s__Nibricoccus aquaticus", "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus", "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_007559335.1", "gtdb_species": "s__Rariglobus hedericola", "ani": 78.6695, "matched_fragments": 339, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus", "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": "GCA_018239845.1", "gtdb_species": "s__Opitutus sp018239845", "ani": 78.4401, "matched_fragments": 343, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus", "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": "GCA_903876795.1", "gtdb_species": "s__Rariglobus sp903876795", "ani": 78.289, "matched_fragments": 282, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus", "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": "GCA_002288455.1", "gtdb_species": "s__ER46 sp002288455", "ani": 78.2097, "matched_fragments": 292, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46", "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": "GCA_016721945.1", "gtdb_species": "s__Nibricoccus sp016721945", "ani": 78.1968, "matched_fragments": 292, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus", "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": "GCA_903839035.1", "gtdb_species": "s__Opi-474 sp903839035", "ani": 78.1819, "matched_fragments": 265, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.67", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_903948415.1", "gtdb_species": "s__CAITWF01 sp903948415", "ani": 78.1525, "matched_fragments": 358, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01", "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": "GCA_903904685.1", "gtdb_species": "s__Rariglobus sp903904685", "ani": 78.062, "matched_fragments": 256, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016715765.1", "gtdb_species": "s__UBA2377 sp016715765", "ani": 77.8681, "matched_fragments": 256, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377", "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": "GCA_016235555.1", "gtdb_species": "s__ER46 sp016235555", "ani": 77.7684, "matched_fragments": 365, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46", "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": "GCA_001650175.1", "gtdb_species": "s__Ereboglobus sp001650175", "ani": 77.7072, "matched_fragments": 372, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus", "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": "GCA_903881475.1", "gtdb_species": "s__Opi-474 sp903881475", "ani": 77.6179, "matched_fragments": 243, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.50", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_903877135.1", "gtdb_species": "s__Opitutus sp903877135", "ani": 77.5639, "matched_fragments": 258, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_903862955.1", "gtdb_species": "s__Opi-474 sp903862955", "ani": 77.548, "matched_fragments": 276, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_003054665.1", "gtdb_species": "s__EW11 sp003054665", "ani": 77.3406, "matched_fragments": 300, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__EW11", "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": "GCA_016871755.1", "gtdb_species": "s__UBA6669 sp016871755", "ani": 77.1726, "matched_fragments": 203, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669", "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": "GCA_903862595.1", "gtdb_species": "s__UBA6669 sp903862595", "ani": 77.1322, "matched_fragments": 157, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_903848965.1", "gtdb_species": "s__ER46 sp903848965", "ani": 76.7367, "matched_fragments": 171, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46", "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": "GCA_014879845.1", "gtdb_species": "s__J108 sp014879845", "ani": 76.6165, "matched_fragments": 237, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Nibricoccus", "aquaticus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }