{
    "type": "genome",
    "identifier": "GCF_000255555.1",
    "organism": "Treponema saccharophilum DSM 2985",
    "title": "Treponema saccharophilum DSM 2985",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "JGI",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000255555.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02261376",
        "wgs_master": "AGRW00000000.1",
        "refseq_category": "na",
        "taxid": "907348",
        "species_taxid": "165",
        "organism_name": "Treponema saccharophilum DSM 2985",
        "infraspecific_name": "strain=DSM 2985",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2012/03/21",
        "asm_name": "ASM25555v2",
        "asm_submitter": "JGI",
        "gbrs_paired_asm": "GCA_000255555.2",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/255/555/GCF_000255555.1_ASM25555v2",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "3453898",
        "genome_size_ungapped": "3453898",
        "gc_percent": "53.000000",
        "replicon_count": "0",
        "scaffold_count": "56",
        "contig_count": "56",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000255555.1-RS_2024_05_01",
        "annotation_date": "2024-05-01",
        "total_gene_count": "2981",
        "protein_coding_gene_count": "2901",
        "non_coding_gene_count": "68",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2012-03-21",
    "dateModified": "2012-03-21",
    "datePublished": "2012-03-21",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Treponema saccharophilum DSM 2985"
        ],
        "sample_taxid": [
            "907348"
        ],
        "sample_host_organism": [
            "Bovine"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [
            "None"
        ],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Missing"
        ],
        "sample_host_location_id": [],
        "data_size": "0.962 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 99.62,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "3453898",
        "Number of Sequences": "56",
        "Longest Sequences (bp)": "314154",
        "N50 (bp)": "138893",
        "Gap Ratio (%)": "0.000029",
        "GCcontent (%)": "53.2",
        "Number of CDSs": "2904",
        "Average Protein Length": "347.1",
        "Coding Ratio (%)": "87.5",
        "Number of rRNAs": "2",
        "Number of tRNAs": "64",
        "Number of CRISPRs": "7"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Treponema saccharophilum",
                "strain": "strain=DSM 2985",
                "accession": "GCA_000255555.2",
                "taxid": 165,
                "species_taxid": 165,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1124,
                "total_fragments": 1127,
                "ani_threshold": 95,
                "status": "conclusive"
            }
        ],
        "cc_result": {
            "completeness": 99.62,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000255555.1",
                "gtdb_species": "s__Treponema_D saccharophilum",
                "ani": 100.0,
                "matched_fragments": 1124,
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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": "99.00",
                "min_intra_species_ani": "98.95",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.97",
                "num_clustered_genomes": 3,
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            },
            {
                "accession": "GCA_017934745.1",
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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": "96.63",
                "min_intra_species_ani": "96.63",
                "mean_intra_species_af": "0.83",
                "min_intra_species_af": "0.83",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_017525605.1",
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                "matched_fragments": 390,
                "total_fragments": 1127,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.48",
                "min_intra_species_ani": "98.48",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_017412405.1",
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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": "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_900316905.1",
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                "total_fragments": 1127,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
                "ani_circumscription_radius": 95.0,
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                "status": "-"
            },
            {
                "accession": "GCA_902783155.1",
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                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
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                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_002404895.1",
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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": "N/A",
                "min_intra_species_ani": "N/A",
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            },
            {
                "accession": "GCA_902799665.1",
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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": "97.67",
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            },
            {
                "accession": "GCA_017450845.1",
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                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D",
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                "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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            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.222,
        "cell_length": 1.079,
        "doubling_h": 0.176,
        "growth_tmp": 37.0,
        "optimum_tmp": 37.0,
        "optimum_ph": 7.183,
        "genome_size": 3449536.0,
        "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": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 1.0
    },
    "_genome_taxon": [
        "Treponema",
        "saccharophilum",
        "DSM",
        "2985"
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}