{
    "type": "genome",
    "identifier": "GCF_000306675.2",
    "organism": "Leptospira mayottensis 200901116",
    "title": "Leptospira mayottensis 200901116",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "J. Craig Venter Institute",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000306675.2",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02436412",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "1192864",
        "species_taxid": "1137606",
        "organism_name": "Leptospira mayottensis 200901116",
        "infraspecific_name": "strain=200901116",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2018/12/21",
        "asm_name": "ASM30667v3",
        "asm_submitter": "J. Craig Venter Institute",
        "gbrs_paired_asm": "GCA_000306675.3",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/306/675/GCF_000306675.2_ASM30667v3",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "4216282",
        "genome_size_ungapped": "4216282",
        "gc_percent": "39.500000",
        "replicon_count": "3",
        "scaffold_count": "3",
        "contig_count": "3",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000306675.2-RS_2024_03_28",
        "annotation_date": "2024-03-28",
        "total_gene_count": "3700",
        "protein_coding_gene_count": "3412",
        "non_coding_gene_count": "44",
        "pubmed_id": "30082683"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2018-12-21",
    "dateModified": "2018-12-21",
    "datePublished": "2018-12-21",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Leptospira mayottensis 200901116"
        ],
        "sample_taxid": [
            "1192864"
        ],
        "sample_host_organism": [
            "Homo sapiens"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Mayotte"
        ],
        "sample_host_location_id": [],
        "data_size": "1.166 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 91.67,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "4216282",
        "Number of Sequences": "3",
        "Longest Sequences (bp)": "3815263",
        "N50 (bp)": "3815263",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "39.6",
        "Number of CDSs": "3538",
        "Average Protein Length": "321.8",
        "Coding Ratio (%)": "81.0",
        "Number of rRNAs": "5",
        "Number of tRNAs": "37",
        "Number of CRISPRs": "4"
    },
    "has_analysis": true,
    "_dfastqc": {
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            {
                "organism_name": "Leptospira mayottensis",
                "strain": "strain=200901116",
                "accession": "GCA_000306675.3",
                "taxid": 1137606,
                "species_taxid": 1137606,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1398,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Leptospira alexanderi",
                "strain": "strain=L 60",
                "accession": "GCA_000243815.3",
                "taxid": 100053,
                "species_taxid": 100053,
                "relation_to_type": "type",
                "validated": true,
                "ani": 91.923,
                "matched_fragments": 1123,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leptospira borgpetersenii",
                "strain": "strain=DSM 21538",
                "accession": "GCA_003046425.1",
                "taxid": 174,
                "species_taxid": 174,
                "relation_to_type": "type",
                "validated": true,
                "ani": 90.988,
                "matched_fragments": 1131,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leptospira santarosai",
                "strain": "strain=LT 821",
                "accession": "GCA_000313175.2",
                "taxid": 28183,
                "species_taxid": 28183,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.7104,
                "matched_fragments": 1054,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leptospira alstonii",
                "strain": "strain=79601",
                "accession": "GCA_000347175.1",
                "taxid": 28452,
                "species_taxid": 28452,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.8938,
                "matched_fragments": 963,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leptospira yasudae",
                "strain": "strain=F1",
                "accession": "GCA_003545925.1",
                "taxid": 2202201,
                "species_taxid": 2202201,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.1756,
                "matched_fragments": 767,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leptospira kirschneri",
                "strain": "strain=3522 CT",
                "accession": "GCA_000243695.3",
                "taxid": 29507,
                "species_taxid": 29507,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.0921,
                "matched_fragments": 878,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Leptospira interrogans",
                "strain": "strain=ATCC 43642",
                "accession": "GCA_900156205.1",
                "taxid": 173,
                "species_taxid": 173,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.9644,
                "matched_fragments": 827,
                "total_fragments": 1404,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 91.67,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000306675.2",
                "gtdb_species": "s__Leptospira mayottensis",
                "ani": 100.0,
                "matched_fragments": 1401,
                "total_fragments": 1404,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.59",
                "min_intra_species_ani": "98.88",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 6,
                "status": "conclusive"
            },
            {
                "accession": "GCF_000243815.2",
                "gtdb_species": "s__Leptospira alexanderi",
                "ani": 91.9036,
                "matched_fragments": 1125,
                "total_fragments": 1404,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.22",
                "min_intra_species_ani": "97.61",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 6,
                "status": "-"
            },
            {
                "accession": "GCF_003046425.1",
                "gtdb_species": "s__Leptospira borgpetersenii",
                "ani": 90.999,
                "matched_fragments": 1130,
                "total_fragments": 1404,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.13",
                "min_intra_species_ani": "97.82",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 148,
                "status": "-"
            },
            {
                "accession": "GCF_000244815.1",
                "gtdb_species": "s__Leptospira weilii",
                "ani": 90.7416,
                "matched_fragments": 1147,
                "total_fragments": 1404,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "95.50",
                "min_intra_species_ani": "95.12",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.84",
                "num_clustered_genomes": 20,
                "status": "-"
            },
            {
                "accession": "GCF_000313175.2",
                "gtdb_species": "s__Leptospira santarosai",
                "ani": 86.7225,
                "matched_fragments": 1051,
                "total_fragments": 1404,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.62",
                "min_intra_species_ani": "96.47",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 43,
                "status": "-"
            },
            {
                "accession": "GCF_000347175.1",
                "gtdb_species": "s__Leptospira alstonii",
                "ani": 82.9126,
                "matched_fragments": 958,
                "total_fragments": 1404,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira",
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                "mean_intra_species_ani": "99.79",
                "min_intra_species_ani": "99.25",
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                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 5,
                "status": "-"
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        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.8,
        "cell_length": 0.954,
        "doubling_h": 1.009,
        "growth_tmp": 29.846,
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        "optimum_ph": 7.4,
        "genome_size": 4170519.75,
        "gc_content": 39.54,
        "coding_genes": 3541.0,
        "rRNA16S_genes": 2.0,
        "tRNA_genes": 37.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": 0.0,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "mesophilic_range_tmp": 1.0,
        "thermophilic_range_tmp": 0.0,
        "psychrophilic_range_tmp": 0.0,
        "bacillus_cell_shape": 0.1,
        "coccus_cell_shape": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.9
    },
    "_genome_taxon": [
        "Leptospira",
        "mayottensis",
        "200901116"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}