{
    "type": "genome",
    "identifier": "GCF_000733935.1",
    "organism": "Methylomarinum vadi",
    "title": "Methylomarinum vadi",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE Joint Genome Institute",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000733935.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02745036",
        "wgs_master": "JPON00000000.1",
        "refseq_category": "reference genome",
        "taxid": "438855",
        "species_taxid": "438855",
        "organism_name": "Methylomarinum vadi",
        "infraspecific_name": "strain=IT-4",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2014/07/24",
        "asm_name": "ASM73393v1",
        "asm_submitter": "DOE Joint Genome Institute",
        "gbrs_paired_asm": "GCA_000733935.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/733/935/GCF_000733935.1_ASM73393v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "4335162",
        "genome_size_ungapped": "4335162",
        "gc_percent": "51.500000",
        "replicon_count": "0",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000733935.1-RS_2024_12_09",
        "annotation_date": "2024-12-09",
        "total_gene_count": "4062",
        "protein_coding_gene_count": "3853",
        "non_coding_gene_count": "61",
        "pubmed_id": "26798114"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2014-07-24",
    "dateModified": "2014-07-24",
    "datePublished": "2014-07-24",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Methylomarinum vadi"
        ],
        "sample_taxid": [
            "438855"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Japan: Taketomi Island, Okinawa"
        ],
        "sample_host_location_id": [],
        "data_size": "1.220 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 98.96,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "4335162",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "4335162",
        "N50 (bp)": "4335162",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "51.3",
        "Number of CDSs": "4013",
        "Average Protein Length": "313.2",
        "Coding Ratio (%)": "87.0",
        "Number of rRNAs": "9",
        "Number of tRNAs": "49",
        "Number of CRISPRs": "3"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Methylomarinum vadi",
                "strain": "strain=IT-4",
                "accession": "GCA_000733935.1",
                "taxid": 438855,
                "species_taxid": 438855,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1444,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Methylomonas koyamae",
                "strain": "strain=Fw12E-Y",
                "accession": "GCA_019669905.1",
                "taxid": 702114,
                "species_taxid": 702114,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 77.5926,
                "matched_fragments": 211,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylomonas denitrificans",
                "strain": "strain=FJG1",
                "accession": "GCA_000785705.2",
                "taxid": 1538553,
                "species_taxid": 1538553,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.4952,
                "matched_fragments": 170,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylomicrobium lacus",
                "strain": "strain=LW14",
                "accession": "GCA_000527095.1",
                "taxid": 136992,
                "species_taxid": 136992,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.483,
                "matched_fragments": 185,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylobacter marinus",
                "strain": "strain=A45",
                "accession": "GCA_000383855.1",
                "taxid": 34058,
                "species_taxid": 34058,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.2344,
                "matched_fragments": 210,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylomonas koyamae",
                "strain": "strain=JCM 16701",
                "accession": "GCA_001312005.1",
                "taxid": 702114,
                "species_taxid": 702114,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 77.1597,
                "matched_fragments": 202,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylomonas albis",
                "strain": "strain=EbA",
                "accession": "GCA_014850955.1",
                "taxid": 1854563,
                "species_taxid": 1854563,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.0717,
                "matched_fragments": 164,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylicorpusculum oleiharenae",
                "strain": "strain=XLMV4",
                "accession": "GCA_009828925.2",
                "taxid": 1338687,
                "species_taxid": 1338687,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.967,
                "matched_fragments": 94,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylobacter tundripaludum",
                "strain": "strain=SV96",
                "accession": "GCA_000190755.3",
                "taxid": 173365,
                "species_taxid": 173365,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.8531,
                "matched_fragments": 136,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylosarcina fibrata",
                "strain": "strain=AML-C10",
                "accession": "GCA_000372865.1",
                "taxid": 105972,
                "species_taxid": 105972,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.8047,
                "matched_fragments": 173,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methylotuvimicrobium alcaliphilum",
                "strain": "strain=20Z",
                "accession": "GCA_000968535.1",
                "taxid": 271065,
                "species_taxid": 271065,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.7606,
                "matched_fragments": 161,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Methyloglobulus morosus",
                "strain": "strain=KoM1",
                "accession": "GCA_000496735.2",
                "taxid": 1410681,
                "species_taxid": 1410681,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.898,
                "matched_fragments": 73,
                "total_fragments": 1445,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 98.96,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000733935.1",
                "gtdb_species": "s__Methylomarinum vadi",
                "ani": 100.0,
                "matched_fragments": 1445,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomarinum",
                "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_015711015.1",
                "gtdb_species": "s__Methylomonas sp015711015",
                "ani": 77.4856,
                "matched_fragments": 222,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "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_000527095.1",
                "gtdb_species": "s__Methylomicrobium lacus",
                "ani": 77.462,
                "matched_fragments": 184,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium",
                "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_000427625.1",
                "gtdb_species": "s__Methylobacter luteus",
                "ani": 77.3817,
                "matched_fragments": 178,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter",
                "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_006483455.1",
                "gtdb_species": "s__Methylomonas koyamae_B",
                "ani": 77.266,
                "matched_fragments": 208,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "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_000214665.1",
                "gtdb_species": "s__Methylomonas methanica_B",
                "ani": 77.2273,
                "matched_fragments": 182,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "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_001312005.1",
                "gtdb_species": "s__Methylomonas koyamae",
                "ani": 77.1459,
                "matched_fragments": 203,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.46",
                "min_intra_species_ani": "95.49",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCF_001644035.1",
                "gtdb_species": "s__Methylomonas methanica_A",
                "ani": 77.1008,
                "matched_fragments": 170,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "95.96",
                "min_intra_species_ani": "95.96",
                "mean_intra_species_af": "0.85",
                "min_intra_species_af": "0.85",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_006788925.1",
                "gtdb_species": "s__Methylotuvimicrobium kenyense",
                "ani": 77.0845,
                "matched_fragments": 176,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium",
                "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_001644045.1",
                "gtdb_species": "s__Methylomonas methanica",
                "ani": 77.083,
                "matched_fragments": 162,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.99",
                "min_intra_species_ani": "99.99",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_016865255.1",
                "gtdb_species": "s__Methylomonas sp000702925",
                "ani": 77.0094,
                "matched_fragments": 175,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.47",
                "min_intra_species_ani": "95.82",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCA_002928965.1",
                "gtdb_species": "s__Methylomonas sp002928965",
                "ani": 76.8049,
                "matched_fragments": 130,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "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_903064685.1",
                "gtdb_species": "s__Methylomonas sp903064685",
                "ani": 76.7864,
                "matched_fragments": 178,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas",
                "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": "-"
            },
            {
                "accession": "GCF_000372865.1",
                "gtdb_species": "s__Methylosarcina fibrata",
                "ani": 76.6824,
                "matched_fragments": 172,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina",
                "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_015476545.1",
                "gtdb_species": "s__Methylobacter sp015476545",
                "ani": 76.5511,
                "matched_fragments": 171,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter",
                "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_003994235.2",
                "gtdb_species": "s__Methylobacter_A oryzae",
                "ani": 76.5464,
                "matched_fragments": 142,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A",
                "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_002299495.1",
                "gtdb_species": "s__Methylovulum sp002299495",
                "ani": 76.2407,
                "matched_fragments": 60,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum",
                "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_016784875.1",
                "gtdb_species": "s__Methylobacter_A sp016784875",
                "ani": 76.1109,
                "matched_fragments": 80,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A",
                "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_004322395.1",
                "gtdb_species": "s__Methylobacter_A sp004322395",
                "ani": 76.0907,
                "matched_fragments": 103,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A",
                "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_004299305.1",
                "gtdb_species": "s__Methylobacter_A sp004299305",
                "ani": 75.9731,
                "matched_fragments": 113,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A",
                "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_002422395.1",
                "gtdb_species": "s__Methylovulum sp002422395",
                "ani": 75.9218,
                "matched_fragments": 81,
                "total_fragments": 1445,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylovulum",
                "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": 0.0,
        "cell_length": 0.29,
        "doubling_h": null,
        "growth_tmp": 37.0,
        "optimum_tmp": 40.0,
        "optimum_ph": 6.4,
        "genome_size": 4335162.0,
        "gc_content": null,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": 0.0,
        "sporulation": null,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "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": [
        "Methylomarinum",
        "vadi"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}