{
    "type": "genome",
    "identifier": "GCA_004556105.1",
    "organism": "Treponema sp.",
    "title": "Treponema sp.",
    "description": "derived from metagenome",
    "data type": "Genome sequencing and assembly",
    "organization": "University of Alberta",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCA_004556105.1",
        "bioproject": "PRJNA494875",
        "biosample": "SAMN10183621",
        "wgs_master": "SFIT00000000.1",
        "refseq_category": "na",
        "taxid": "166",
        "species_taxid": "166",
        "organism_name": "Treponema sp.",
        "infraspecific_name": "",
        "isolate": "W1P25.018",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2019/04/01",
        "asm_name": "ASM455610v1",
        "submitter": "University of Alberta",
        "gbrs_paired_asm": "na",
        "paired_asm_comp": "na",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/556/105/GCA_004556105.1_ASM455610v1",
        "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": "2019-04-01",
    "dateModified": "2019-04-01",
    "datePublished": "2019-04-01",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Treponema sp."
        ],
        "sample_taxid": [
            "166"
        ],
        "sample_host_organism": [
            "Sus scrofa"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Canada: Edmonton"
        ],
        "sample_host_location_id": [],
        "data_size": "0.594 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 72.92,
        "contamination": 8.33,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "MAG",
    "data_source": "INSDC",
    "_dfast": {
        "Total Sequence Length (bp)": "2110065",
        "Number of Sequences": "128",
        "Longest Sequences (bp)": "89391",
        "N50 (bp)": "22791",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "43.9",
        "Number of CDSs": "1731",
        "Average Protein Length": "344.9",
        "Coding Ratio (%)": "84.9",
        "Number of rRNAs": "0",
        "Number of tRNAs": "40",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
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            {
                "organism_name": "Treponema porcinum",
                "strain": "strain=ATCC BAA-908",
                "accession": "GCA_900167145.1",
                "taxid": 261392,
                "species_taxid": 261392,
                "relation_to_type": "type",
                "validated": true,
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                "total_fragments": 642,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Treponema succinifaciens",
                "strain": "strain=DSM 2489",
                "accession": "GCA_000195275.1",
                "taxid": 167,
                "species_taxid": 167,
                "relation_to_type": "type",
                "validated": true,
                "ani": 85.5609,
                "matched_fragments": 115,
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                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Treponema peruense",
                "strain": "strain=RCC2812",
                "accession": "GCA_016117655.1",
                "taxid": 2787628,
                "species_taxid": 2787628,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.4584,
                "matched_fragments": 72,
                "total_fragments": 642,
                "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": 76.0026,
                "matched_fragments": 66,
                "total_fragments": 642,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 72.92,
            "contamination": 8.33,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900167145.1",
                "gtdb_species": "s__Treponema_D porcinum",
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                "matched_fragments": 582,
                "total_fragments": 642,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.53",
                "min_intra_species_ani": "96.24",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 5,
                "status": "conclusive"
            },
            {
                "accession": "GCA_900541945.1",
                "gtdb_species": "s__Treponema_D sp900541945",
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                "matched_fragments": 156,
                "total_fragments": 642,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.94",
                "min_intra_species_ani": "97.90",
                "mean_intra_species_af": "0.88",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_900769325.1",
                "gtdb_species": "s__Treponema_D sp900769325",
                "ani": 77.6409,
                "matched_fragments": 127,
                "total_fragments": 642,
                "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_002437725.1",
                "gtdb_species": "s__Treponema_D sp002437725",
                "ani": 77.5441,
                "matched_fragments": 92,
                "total_fragments": 642,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.48",
                "min_intra_species_ani": "98.76",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.84",
                "num_clustered_genomes": 13,
                "status": "-"
            },
            {
                "accession": "GCA_900317625.1",
                "gtdb_species": "s__Treponema_D sp900317625",
                "ani": 77.4957,
                "matched_fragments": 123,
                "total_fragments": 642,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.21",
                "min_intra_species_ani": "99.03",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_002478955.1",
                "gtdb_species": "s__Treponema_D sp002478955",
                "ani": 77.3772,
                "matched_fragments": 120,
                "total_fragments": 642,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.79",
                "min_intra_species_ani": "97.79",
                "mean_intra_species_af": "0.82",
                "min_intra_species_af": "0.82",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_017381365.1",
                "gtdb_species": "s__Treponema_D sp017381365",
                "ani": 77.2065,
                "matched_fragments": 108,
                "total_fragments": 642,
                "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_017470605.1",
                "gtdb_species": "s__Treponema_D sp017470605",
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                "matched_fragments": 71,
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                "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,
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            },
            {
                "accession": "GCA_902797305.1",
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                "matched_fragments": 75,
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                "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,
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            },
            {
                "accession": "GCA_017386165.1",
                "gtdb_species": "s__Treponema_D sp017386165",
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                "mean_intra_species_ani": "N/A",
                "min_intra_species_ani": "N/A",
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                "num_clustered_genomes": 1,
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            },
            {
                "accession": "GCA_014803985.1",
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                "min_intra_species_ani": "97.81",
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            },
            {
                "accession": "GCA_002350445.1",
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                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.37",
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                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.59,
        "cell_length": 0.834,
        "doubling_h": 0.49,
        "growth_tmp": 35.047,
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        "genome_size": 2974429.677,
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        "coding_genes": 2837.944,
        "rRNA16S_genes": 2.285,
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        "gram_stain": 0.0,
        "sporulation": 0.0,
        "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": 0.055,
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        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.055,
        "spiral_cell_shape": 0.888
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    "_gtdb_taxon": [
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        "p__Spirochaetota",
        "c__Spirochaetia",
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        "g__Treponema_D",
        "s__Treponema_D porcinum"
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    "_genome_taxon": [
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        "sp.",
        "d__Bacteria",
        "p__Spirochaetota",
        "c__Spirochaetia",
        "o__Treponematales",
        "f__Treponemataceae",
        "g__Treponema_D",
        "s__Treponema_D porcinum",
        "Bacteria",
        "Spirochaetota",
        "Spirochaetia",
        "Treponematales",
        "Treponemataceae",
        "Treponema",
        "D",
        "Treponema",
        "D",
        "porcinum"
    ],
    "_meo": [
        {
            "id": "MEO_0000054",
            "label": "feces"
        }
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}