{
    "type": "genome",
    "identifier": "GCF_017161325.1",
    "organism": "Treponema pedis",
    "title": "Treponema pedis",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "University of Liverpool",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_017161325.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN09783521",
        "wgs_master": "na",
        "refseq_category": "na",
        "taxid": "409322",
        "species_taxid": "409322",
        "organism_name": "Treponema pedis",
        "infraspecific_name": "strain=T3552B",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2021/03/03",
        "asm_name": "ASM1716132v1",
        "asm_submitter": "University of Liverpool",
        "gbrs_paired_asm": "GCA_017161325.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/161/325/GCF_017161325.1_ASM1716132v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2889390",
        "genome_size_ungapped": "2889390",
        "gc_percent": "37.000000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_017161325.1-RS_2024_07_06",
        "annotation_date": "2024-07-06",
        "total_gene_count": "2737",
        "protein_coding_gene_count": "2561",
        "non_coding_gene_count": "54",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2021-03-03",
    "dateModified": "2021-03-03",
    "datePublished": "2021-03-03",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Treponema pedis"
        ],
        "sample_taxid": [
            "409322"
        ],
        "sample_host_organism": [
            "Bos taurus"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "United Kingdom: Merseyside"
        ],
        "sample_host_location_id": [],
        "data_size": "0.794 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)": "2889390",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "2889390",
        "N50 (bp)": "2889390",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "36.9",
        "Number of CDSs": "2723",
        "Average Protein Length": "308.7",
        "Coding Ratio (%)": "87.3",
        "Number of rRNAs": "6",
        "Number of tRNAs": "45",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
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                "organism_name": "Treponema pedis",
                "strain": "strain=T3552B",
                "accession": "GCA_017161325.1",
                "taxid": 409322,
                "species_taxid": 409322,
                "relation_to_type": "type",
                "validated": true,
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                "matched_fragments": 963,
                "total_fragments": 963,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Treponema denticola",
                "strain": "strain=ATCC 35405",
                "accession": "GCA_000008185.1",
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                "species_taxid": 158,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3352,
                "matched_fragments": 220,
                "total_fragments": 963,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema putidum",
                "strain": "strain=OMZ 758",
                "accession": "GCA_000755145.1",
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                "species_taxid": 221027,
                "relation_to_type": "type",
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                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema putidum",
                "strain": "strain=ATCC 700334",
                "accession": "GCA_007830595.1",
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                "species_taxid": 221027,
                "relation_to_type": "type",
                "validated": true,
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                "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": 76.7351,
                "matched_fragments": 69,
                "total_fragments": 963,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 98.96,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_017161325.1",
                "gtdb_species": "s__Treponema_B pedis",
                "ani": 100.0,
                "matched_fragments": 963,
                "total_fragments": 963,
                "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": "conclusive"
            },
            {
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                "matched_fragments": 220,
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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": "97.58",
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                "num_clustered_genomes": 17,
                "status": "-"
            },
            {
                "accession": "GCF_000755145.1",
                "gtdb_species": "s__Treponema_B putidum",
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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": "99.99",
                "min_intra_species_ani": "99.99",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 2,
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            },
            {
                "accession": "GCF_000413095.1",
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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": "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",
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                "ani": 77.4778,
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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": "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_008153345.1",
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                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema",
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                "mean_intra_species_ani": "99.50",
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                "num_clustered_genomes": 14,
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            }
        ]
    },
    "_bac2feature": {
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        "bacillus_cell_shape": 0.0,
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    "_genome_taxon": [
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    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}