{
    "type": "genome",
    "identifier": "GCF_000013025.1",
    "organism": "Hyphomonas neptunium ATCC 15444",
    "title": "Hyphomonas neptunium ATCC 15444",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "TIGR",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000013025.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02604041",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "228405",
        "species_taxid": "81032",
        "organism_name": "Hyphomonas neptunium ATCC 15444",
        "infraspecific_name": "strain=ATCC 15444",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2006/09/18",
        "asm_name": "ASM1302v1",
        "asm_submitter": "TIGR",
        "gbrs_paired_asm": "GCA_000013025.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/013/025/GCF_000013025.1_ASM1302v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "3705021",
        "genome_size_ungapped": "3705021",
        "gc_percent": "62.000000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000013025.1-RS_2024_12_09",
        "annotation_date": "2024-12-09",
        "total_gene_count": "3565",
        "protein_coding_gene_count": "3497",
        "non_coding_gene_count": "49",
        "pubmed_id": "16980487"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2006-09-18",
    "dateModified": "2006-09-18",
    "datePublished": "2006-09-18",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Hyphomonas neptunium ATCC 15444"
        ],
        "sample_taxid": [
            "228405"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "1.036 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)": "3705021",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "3705021",
        "N50 (bp)": "3705021",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "61.9",
        "Number of CDSs": "3519",
        "Average Protein Length": "318.1",
        "Coding Ratio (%)": "90.6",
        "Number of rRNAs": "3",
        "Number of tRNAs": "46",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Hyphomonas polymorpha",
                "strain": "strain=PS728",
                "accession": "GCA_000685315.1",
                "taxid": 74319,
                "species_taxid": 74319,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.2803,
                "matched_fragments": 926,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas sediminis",
                "strain": "strain=WL0036",
                "accession": "GCA_019679475.1",
                "taxid": 2866160,
                "species_taxid": 2866160,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.7314,
                "matched_fragments": 828,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas chukchiensis",
                "strain": "strain=BH-BN04-4",
                "accession": "GCA_000682695.1",
                "taxid": 1280947,
                "species_taxid": 1280947,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3661,
                "matched_fragments": 382,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas jannaschiana",
                "strain": "strain=VP2",
                "accession": "GCA_000685215.1",
                "taxid": 86,
                "species_taxid": 86,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.1961,
                "matched_fragments": 422,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas oceanitis",
                "strain": "strain=SCH89",
                "accession": "GCA_000685295.1",
                "taxid": 81033,
                "species_taxid": 81033,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.1386,
                "matched_fragments": 365,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas adhaerens",
                "strain": "strain=MHS-3",
                "accession": "GCA_000685235.1",
                "taxid": 81029,
                "species_taxid": 81029,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.0769,
                "matched_fragments": 394,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas johnsonii",
                "strain": "strain=MHS-2",
                "accession": "GCA_000685275.1",
                "taxid": 81031,
                "species_taxid": 81031,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9859,
                "matched_fragments": 376,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Hyphomonas beringensis",
                "strain": "strain=25B14_1",
                "accession": "GCA_000682755.1",
                "taxid": 1280946,
                "species_taxid": 1280946,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.8875,
                "matched_fragments": 321,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Henriciella aquimarina",
                "strain": "strain=LMG 24711",
                "accession": "GCA_002088975.1",
                "taxid": 545261,
                "species_taxid": 545261,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.399,
                "matched_fragments": 255,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Henriciella pelagia",
                "strain": "strain=LA220",
                "accession": "GCA_002088945.1",
                "taxid": 1977912,
                "species_taxid": 1977912,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.2786,
                "matched_fragments": 200,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Henriciella pelagia",
                "strain": "strain=CGMCC 1.15928",
                "accession": "GCA_014644035.1",
                "taxid": 1977912,
                "species_taxid": 1977912,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.2643,
                "matched_fragments": 197,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Henriciella marina",
                "strain": "strain=DSM 19595",
                "accession": "GCA_000376805.1",
                "taxid": 453851,
                "species_taxid": 453851,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.9159,
                "matched_fragments": 197,
                "total_fragments": 1235,
                "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": 76.2084,
                "matched_fragments": 94,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shinella pollutisoli",
                "strain": "strain=KCTC 52677",
                "accession": "GCA_024609765.1",
                "taxid": 2250594,
                "species_taxid": 2250594,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.0633,
                "matched_fragments": 113,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylobacterium tardum",
                "strain": "strain=DSM 19566",
                "accession": "GCA_023546765.1",
                "taxid": 374432,
                "species_taxid": 374432,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.9931,
                "matched_fragments": 105,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylobacterium tardum",
                "strain": "strain=NBRC 103632",
                "accession": "GCA_022179585.1",
                "taxid": 374432,
                "species_taxid": 374432,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.8315,
                "matched_fragments": 100,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Lichenibacterium minor",
                "strain": "strain=RmlP026",
                "accession": "GCA_004137685.1",
                "taxid": 2316528,
                "species_taxid": 2316528,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.5955,
                "matched_fragments": 91,
                "total_fragments": 1235,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000013025.1",
                "gtdb_species": "s__Hyphomonas neptunium",
                "ani": 100.0,
                "matched_fragments": 1235,
                "total_fragments": 1235,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "100.00",
                "min_intra_species_ani": "100.00",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 2,
                "status": "conclusive"
            },
            {
                "accession": "GCA_002841155.1",
                "gtdb_species": "s__Hyphomonas sp002841155",
                "ani": 86.1289,
                "matched_fragments": 945,
                "total_fragments": 1235,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas",
                "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_018402285.1",
                "gtdb_species": "s__Hyphomonas sp018402285",
                "ani": 84.8897,
                "matched_fragments": 798,
                "total_fragments": 1235,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas",
                "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_013823385.1",
                "gtdb_species": "s__Hyphomonas sp013823385",
                "ani": 84.8764,
                "matched_fragments": 901,
                "total_fragments": 1235,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas",
                "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_002282565.1",
                "gtdb_species": "s__Hyphomonas sp002282565",
                "ani": 84.2898,
                "matched_fragments": 662,
                "total_fragments": 1235,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas",
                "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_000685315.1",
                "gtdb_species": "s__Hyphomonas polymorpha",
                "ani": 84.2697,
                "matched_fragments": 927,
                "total_fragments": 1235,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.45",
                "min_intra_species_ani": "98.45",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.489,
        "cell_length": 0.0,
        "doubling_h": null,
        "growth_tmp": 26.0,
        "optimum_tmp": 37.0,
        "optimum_ph": null,
        "genome_size": 3705020.8,
        "gc_content": 61.9,
        "coding_genes": 3467.333,
        "rRNA16S_genes": 1.0,
        "tRNA_genes": 43.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "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": 0.0,
        "spiral_cell_shape": 0.0
    },
    "_genome_taxon": [
        "Hyphomonas",
        "neptunium",
        "ATCC",
        "15444"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}