{
    "type": "genome",
    "identifier": "GCA_018064905.1",
    "organism": "Treponema sp.",
    "title": "Treponema sp.",
    "description": "derived from metagenome",
    "data type": "Genome sequencing and assembly",
    "organization": "Quadram Institute",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCA_018064905.1",
        "bioproject": "PRJNA590977",
        "biosample": "SAMN18472520",
        "wgs_master": "JAGHUJ000000000.1",
        "refseq_category": "na",
        "taxid": "166",
        "species_taxid": "166",
        "organism_name": "Treponema sp.",
        "infraspecific_name": "",
        "isolate": "E4_MB2_2",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2021/04/17",
        "asm_name": "ASM1806490v1",
        "submitter": "Quadram Institute",
        "gbrs_paired_asm": "na",
        "paired_asm_comp": "na",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/064/905/GCA_018064905.1_ASM1806490v1",
        "excluded_from_refseq": "derived from metagenome",
        "relation_to_type_material": "",
        "asm_not_live_date": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2021-04-17",
    "dateModified": "2021-04-17",
    "datePublished": "2021-04-17",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Treponema sp."
        ],
        "sample_taxid": [
            "166"
        ],
        "sample_host_organism": [
            "Equus ferus caballus"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "United Kingdom:Surrey"
        ],
        "sample_host_location_id": [],
        "data_size": "0.792 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 93.94,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "MAG",
    "data_source": "INSDC",
    "_dfast": {
        "Total Sequence Length (bp)": "2807639",
        "Number of Sequences": "223",
        "Longest Sequences (bp)": "93710",
        "N50 (bp)": "19645",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "40.2",
        "Number of CDSs": "2228",
        "Average Protein Length": "352.4",
        "Coding Ratio (%)": "83.9",
        "Number of rRNAs": "0",
        "Number of tRNAs": "32",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Treponema ruminis",
                "strain": "strain=DSM 103462",
                "accession": "GCA_014201975.1",
                "taxid": 744515,
                "species_taxid": 744515,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9334,
                "matched_fragments": 185,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema berlinense",
                "strain": "strain=ATCC BAA-909",
                "accession": "GCA_900167025.1",
                "taxid": 225004,
                "species_taxid": 225004,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.5822,
                "matched_fragments": 124,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema rectale",
                "strain": "strain=DSM 103679",
                "accession": "GCA_014202035.1",
                "taxid": 744512,
                "species_taxid": 744512,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 76.4376,
                "matched_fragments": 66,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 93.94,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCA_018064905.1",
                "gtdb_species": "s__Treponema_D sp018064905",
                "ani": 100.0,
                "matched_fragments": 813,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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": "GCA_016297415.1",
                "gtdb_species": "s__Treponema_D sp016297415",
                "ani": 79.0543,
                "matched_fragments": 176,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_017161305.1",
                "gtdb_species": "s__Treponema_D ruminis",
                "ani": 78.0526,
                "matched_fragments": 156,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.98",
                "min_intra_species_ani": "99.98",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_017381365.1",
                "gtdb_species": "s__Treponema_D sp017381365",
                "ani": 77.8062,
                "matched_fragments": 110,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.14",
                "min_intra_species_ani": "97.14",
                "mean_intra_species_af": "0.75",
                "min_intra_species_af": "0.75",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_016293495.1",
                "gtdb_species": "s__Treponema_D sp016293495",
                "ani": 77.6047,
                "matched_fragments": 85,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.53",
                "min_intra_species_ani": "98.51",
                "mean_intra_species_af": "0.86",
                "min_intra_species_af": "0.85",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_900167025.1",
                "gtdb_species": "s__Treponema_D berlinense",
                "ani": 77.5822,
                "matched_fragments": 124,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.85",
                "min_intra_species_ani": "98.81",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_016283615.1",
                "gtdb_species": "s__Treponema_D sp016283615",
                "ani": 77.5272,
                "matched_fragments": 121,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_002477955.1",
                "gtdb_species": "s__Treponema_D sp002477955",
                "ani": 77.4993,
                "matched_fragments": 98,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.57",
                "min_intra_species_ani": "99.37",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 7,
                "status": "-"
            },
            {
                "accession": "GCA_018385415.1",
                "gtdb_species": "s__Treponema_D sp018385415",
                "ani": 77.448,
                "matched_fragments": 88,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_017430385.1",
                "gtdb_species": "s__Treponema_D sp017430385",
                "ani": 77.4313,
                "matched_fragments": 149,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_018384055.1",
                "gtdb_species": "s__Treponema_D sp018384055",
                "ani": 77.4167,
                "matched_fragments": 92,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.95",
                "min_intra_species_ani": "98.78",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_002404895.1",
                "gtdb_species": "s__Treponema_D sp002404895",
                "ani": 77.3805,
                "matched_fragments": 135,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_014737315.1",
                "gtdb_species": "s__Treponema_D zioleckii",
                "ani": 77.3395,
                "matched_fragments": 115,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_017484285.1",
                "gtdb_species": "s__Treponema_D sp017484285",
                "ani": 77.2137,
                "matched_fragments": 80,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_016293645.1",
                "gtdb_species": "s__Treponema_D sp016293645",
                "ani": 77.1642,
                "matched_fragments": 82,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_004554075.1",
                "gtdb_species": "s__Treponema_D sp004554075",
                "ani": 77.1598,
                "matched_fragments": 80,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_902803735.1",
                "gtdb_species": "s__Treponema_D sp902803735",
                "ani": 77.0868,
                "matched_fragments": 66,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_002392405.1",
                "gtdb_species": "s__Treponema_D sp002392405",
                "ani": 76.9876,
                "matched_fragments": 92,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.78",
                "min_intra_species_ani": "97.78",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_016294035.1",
                "gtdb_species": "s__Treponema_D sp016294035",
                "ani": 76.911,
                "matched_fragments": 88,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.69",
                "min_intra_species_ani": "98.66",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_902789325.1",
                "gtdb_species": "s__Treponema_D sp902789325",
                "ani": 76.7604,
                "matched_fragments": 85,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_018385315.1",
                "gtdb_species": "s__Treponema_D sp018385315",
                "ani": 76.6566,
                "matched_fragments": 76,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_002394465.1",
                "gtdb_species": "s__Treponema_D sp002394465",
                "ani": 76.5931,
                "matched_fragments": 92,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_014202035.1",
                "gtdb_species": "s__Treponema_D rectale",
                "ani": 76.4433,
                "matched_fragments": 67,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.45",
                "min_intra_species_ani": "97.19",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_017962415.1",
                "gtdb_species": "s__Treponema_D sp017962415",
                "ani": 76.2903,
                "matched_fragments": 54,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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_016282835.1",
                "gtdb_species": "s__Treponema_D sp016282835",
                "ani": 76.0372,
                "matched_fragments": 54,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "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": -0.59,
        "cell_length": 0.834,
        "doubling_h": 0.49,
        "growth_tmp": 35.047,
        "optimum_tmp": 33.75,
        "optimum_ph": 7.183,
        "genome_size": 2974429.677,
        "gc_content": 43.752,
        "coding_genes": 2837.944,
        "rRNA16S_genes": 2.285,
        "tRNA_genes": 45.166,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 1.0,
        "aerobic_respiration": 0.0,
        "mesophilic_range_tmp": 1.0,
        "thermophilic_range_tmp": 0.0,
        "psychrophilic_range_tmp": 0.0,
        "bacillus_cell_shape": 0.0,
        "coccus_cell_shape": 0.055,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.055,
        "spiral_cell_shape": 0.888
    },
    "_gtdb_taxon": [
        "d__Bacteria",
        "p__Spirochaetota",
        "c__Spirochaetia",
        "o__Treponematales",
        "f__Treponemataceae",
        "g__Treponema_D",
        "s__Treponema_D sp018064905"
    ],
    "_genome_taxon": [
        "Treponema",
        "sp.",
        "d__Bacteria",
        "p__Spirochaetota",
        "c__Spirochaetia",
        "o__Treponematales",
        "f__Treponemataceae",
        "g__Treponema_D",
        "s__Treponema_D sp018064905",
        "Bacteria",
        "Spirochaetota",
        "Spirochaetia",
        "Treponematales",
        "Treponemataceae",
        "Treponema",
        "D",
        "Treponema",
        "D",
        "sp018064905"
    ],
    "_meo": [
        {
            "id": "MEO_0000054",
            "label": "feces"
        }
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}