{
    "type": "genome",
    "identifier": "GCF_000008185.1",
    "organism": "Treponema denticola ATCC 35405",
    "title": "Treponema denticola ATCC 35405",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "TIGR",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000008185.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02603967",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "243275",
        "species_taxid": "158",
        "organism_name": "Treponema denticola ATCC 35405",
        "infraspecific_name": "strain=ATCC 35405",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2004/02/03",
        "asm_name": "ASM818v1",
        "asm_submitter": "TIGR",
        "gbrs_paired_asm": "GCA_000008185.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/185/GCF_000008185.1_ASM818v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2843201",
        "genome_size_ungapped": "2843201",
        "gc_percent": "38.000000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000008185.1-RS_2024_05_01",
        "annotation_date": "2024-05-01",
        "total_gene_count": "2629",
        "protein_coding_gene_count": "2542",
        "non_coding_gene_count": "53",
        "pubmed_id": "15064399"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2004-02-03",
    "dateModified": "2004-02-03",
    "datePublished": "2004-02-03",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Treponema denticola ATCC 35405"
        ],
        "sample_taxid": [
            "243275"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "0.792 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)": "2843201",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "2843201",
        "N50 (bp)": "2843201",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "37.9",
        "Number of CDSs": "2582",
        "Average Protein Length": "335.9",
        "Coding Ratio (%)": "91.5",
        "Number of rRNAs": "6",
        "Number of tRNAs": "44",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Treponema denticola",
                "strain": "strain=ATCC 35405",
                "accession": "GCA_000008185.1",
                "taxid": 158,
                "species_taxid": 158,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 947,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Treponema putidum",
                "strain": "strain=ATCC 700334",
                "accession": "GCA_007830595.1",
                "taxid": 221027,
                "species_taxid": 221027,
                "relation_to_type": "type",
                "validated": true,
                "ani": 88.9549,
                "matched_fragments": 724,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema putidum",
                "strain": "strain=OMZ 758",
                "accession": "GCA_000755145.1",
                "taxid": 221027,
                "species_taxid": 221027,
                "relation_to_type": "type",
                "validated": true,
                "ani": 88.9473,
                "matched_fragments": 746,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema medium",
                "strain": "strain=ATCC 700293",
                "accession": "GCA_000413035.1",
                "taxid": 58231,
                "species_taxid": 58231,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.7747,
                "matched_fragments": 106,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema maltophilum",
                "strain": "strain=ATCC 51939",
                "accession": "GCA_000413055.1",
                "taxid": 51160,
                "species_taxid": 51160,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.4288,
                "matched_fragments": 60,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema pedis",
                "strain": "strain=T3552B",
                "accession": "GCA_017161325.1",
                "taxid": 409322,
                "species_taxid": 409322,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3645,
                "matched_fragments": 233,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema phagedenis",
                "strain": "strain=B43.1",
                "accession": "GCA_008153345.1",
                "taxid": 162,
                "species_taxid": 162,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.0468,
                "matched_fragments": 64,
                "total_fragments": 947,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000008185.1",
                "gtdb_species": "s__Treponema_B denticola",
                "ani": 100.0,
                "matched_fragments": 947,
                "total_fragments": 947,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.58",
                "min_intra_species_ani": "96.70",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 17,
                "status": "conclusive"
            },
            {
                "accession": "GCF_000413095.1",
                "gtdb_species": "s__Treponema_B denticola_A",
                "ani": 93.6432,
                "matched_fragments": 783,
                "total_fragments": 947,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.93",
                "min_intra_species_ani": "99.93",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_905372345.1",
                "gtdb_species": "s__Treponema_B sp905372345",
                "ani": 92.0896,
                "matched_fragments": 401,
                "total_fragments": 947,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B",
                "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_000755145.1",
                "gtdb_species": "s__Treponema_B putidum",
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                "matched_fragments": 746,
                "total_fragments": 947,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B",
                "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": "1.00",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_017161325.1",
                "gtdb_species": "s__Treponema_B pedis",
                "ani": 78.3147,
                "matched_fragments": 232,
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                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.52",
                "min_intra_species_ani": "98.29",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 7,
                "status": "-"
            },
            {
                "accession": "GCF_000412995.1",
                "gtdb_species": "s__Treponema vincentii",
                "ani": 78.2852,
                "matched_fragments": 91,
                "total_fragments": 947,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.95",
                "min_intra_species_ani": "97.95",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.745,
        "cell_length": 0.832,
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        "growth_tmp": 37.0,
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        "gc_content": 37.868,
        "coding_genes": 2767.0,
        "rRNA16S_genes": 2.0,
        "tRNA_genes": 44.0,
        "gram_stain": 0.0,
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        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.0,
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        "mesophilic_range_tmp": 1.0,
        "thermophilic_range_tmp": 0.0,
        "psychrophilic_range_tmp": 0.0,
        "bacillus_cell_shape": 0.0,
        "coccus_cell_shape": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 1.0
    },
    "_genome_taxon": [
        "Treponema",
        "denticola",
        "ATCC",
        "35405"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}