{
    "type": "genome",
    "identifier": "GCF_017876775.1",
    "organism": "Mycolicibacterium lutetiense",
    "title": "Mycolicibacterium lutetiense",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE Joint Genome Institute",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_017876775.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN17673454",
        "wgs_master": "JAGIOP000000000.1",
        "refseq_category": "reference genome",
        "taxid": "1641992",
        "species_taxid": "1641992",
        "organism_name": "Mycolicibacterium lutetiense",
        "infraspecific_name": "strain=DSM 46713",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2021/04/08",
        "asm_name": "ASM1787677v1",
        "asm_submitter": "DOE Joint Genome Institute",
        "gbrs_paired_asm": "GCA_017876775.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/876/775/GCF_017876775.1_ASM1787677v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "6345289",
        "genome_size_ungapped": "6345289",
        "gc_percent": "66.000000",
        "replicon_count": "0",
        "scaffold_count": "3",
        "contig_count": "3",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_017876775.1-RS_2024_12_09",
        "annotation_date": "2024-12-09",
        "total_gene_count": "6182",
        "protein_coding_gene_count": "5974",
        "non_coding_gene_count": "90",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2021-04-08",
    "dateModified": "2021-04-08",
    "datePublished": "2021-04-08",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Mycolicibacterium lutetiense"
        ],
        "sample_taxid": [
            "1641992"
        ],
        "sample_host_organism": [
            "not applicable"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "missing"
        ],
        "sample_host_location_id": [],
        "data_size": "1.747 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 100.0,
        "contamination": 0.38,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "6345289",
        "Number of Sequences": "3",
        "Longest Sequences (bp)": "4375269",
        "N50 (bp)": "4375269",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "66.0",
        "Number of CDSs": "6170",
        "Average Protein Length": "314.7",
        "Coding Ratio (%)": "91.8",
        "Number of rRNAs": "9",
        "Number of tRNAs": "84",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Mycolicibacterium lutetiense",
                "strain": "strain=DSM 46713",
                "accession": "GCA_017876775.1",
                "taxid": 1641992,
                "species_taxid": 1641992,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 2110,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Mycolicibacterium alvei",
                "strain": "strain=JCM 12272",
                "accession": "GCA_010727325.1",
                "taxid": 67081,
                "species_taxid": 67081,
                "relation_to_type": "type",
                "validated": true,
                "ani": 91.8869,
                "matched_fragments": 1609,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium peregrinum",
                "strain": "strain=DSM 43271",
                "accession": "GCA_002102345.1",
                "taxid": 43304,
                "species_taxid": 43304,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.9164,
                "matched_fragments": 1602,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium septicum",
                "strain": "strain=type strain: DSM 44393",
                "accession": "GCA_000455325.1",
                "taxid": 98668,
                "species_taxid": 98668,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.7394,
                "matched_fragments": 1617,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium septicum",
                "strain": "strain=ATCC 700731",
                "accession": "GCA_012396425.1",
                "taxid": 98668,
                "species_taxid": 98668,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.7245,
                "matched_fragments": 1591,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium nivoides",
                "strain": "strain=DL90",
                "accession": "GCA_003855255.1",
                "taxid": 2487344,
                "species_taxid": 2487344,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.5449,
                "matched_fragments": 1564,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium neworleansense",
                "strain": "strain=type strain: ATCC 49404",
                "accession": "GCA_001245615.1",
                "taxid": 146018,
                "species_taxid": 146018,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.9637,
                "matched_fragments": 1553,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium boenickei",
                "strain": "strain=JCM 15653",
                "accession": "GCA_010731295.1",
                "taxid": 146017,
                "species_taxid": 146017,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.8441,
                "matched_fragments": 1554,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium fortuitum subsp. acetamidolyticum",
                "strain": "strain=JCM6368",
                "accession": "GCA_001570465.1",
                "taxid": 144550,
                "species_taxid": 1766,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.45,
                "matched_fragments": 1527,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium fortuitum subsp. fortuitum",
                "strain": "strain=JCM 6387",
                "accession": "GCA_022179545.1",
                "taxid": 144549,
                "species_taxid": 1766,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.4329,
                "matched_fragments": 1556,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium houstonense",
                "strain": "strain=type strain: ATCC 49403",
                "accession": "GCA_900078665.2",
                "taxid": 146021,
                "species_taxid": 146021,
                "relation_to_type": "type",
                "validated": true,
                "ani": 85.4401,
                "matched_fragments": 1472,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium llatzerense",
                "strain": "strain=MG13",
                "accession": "GCA_025331195.1",
                "taxid": 280871,
                "species_taxid": 280871,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.0745,
                "matched_fragments": 852,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Candidatus Mycolicibacterium alkanivorans",
                "strain": "",
                "accession": "GCA_022760805.1",
                "taxid": 2954114,
                "species_taxid": 2954114,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.8278,
                "matched_fragments": 629,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium mengxianglii",
                "strain": "strain=Z-34",
                "accession": "GCA_015710575.2",
                "taxid": 2736649,
                "species_taxid": 2736649,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.5464,
                "matched_fragments": 705,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycobacterium crocinum",
                "strain": "strain=JCM 16369",
                "accession": "GCA_022370635.3",
                "taxid": 388459,
                "species_taxid": 388459,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.5067,
                "matched_fragments": 823,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycobacterium pallens",
                "strain": "strain=JCM 16370",
                "accession": "GCA_019456675.1",
                "taxid": 370524,
                "species_taxid": 370524,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.4577,
                "matched_fragments": 832,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium vinylchloridicum",
                "strain": "strain=CECT 8761",
                "accession": "GCA_013404075.1",
                "taxid": 2736928,
                "species_taxid": 2736928,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.4486,
                "matched_fragments": 827,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Mycolicibacterium stellerae",
                "strain": "strain=CECT 8783",
                "accession": "GCA_003719305.1",
                "taxid": 2358193,
                "species_taxid": 2358193,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.156,
                "matched_fragments": 803,
                "total_fragments": 2114,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.38,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_017876775.1",
                "gtdb_species": "s__Mycobacterium lutetiense",
                "ani": 100.0,
                "matched_fragments": 2110,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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": "conclusive"
            },
            {
                "accession": "GCF_010727325.1",
                "gtdb_species": "s__Mycobacterium alvei",
                "ani": 91.8825,
                "matched_fragments": 1610,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_011745145.1",
                "gtdb_species": "s__Mycobacterium sp011745145",
                "ani": 89.4211,
                "matched_fragments": 1557,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_001665625.1",
                "gtdb_species": "s__Mycobacterium peregrinum_B",
                "ani": 88.1275,
                "matched_fragments": 1543,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.32",
                "min_intra_species_ani": "98.32",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001665785.1",
                "gtdb_species": "s__Mycobacterium peregrinum_A",
                "ani": 87.9972,
                "matched_fragments": 1562,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_002102345.1",
                "gtdb_species": "s__Mycobacterium peregrinum",
                "ani": 87.9053,
                "matched_fragments": 1605,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.04",
                "min_intra_species_ani": "98.27",
                "mean_intra_species_af": "0.94",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCF_000455325.1",
                "gtdb_species": "s__Mycobacterium septicum",
                "ani": 87.7285,
                "matched_fragments": 1618,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.04",
                "min_intra_species_ani": "95.11",
                "mean_intra_species_af": "0.88",
                "min_intra_species_af": "0.83",
                "num_clustered_genomes": 8,
                "status": "-"
            },
            {
                "accession": "GCF_004762045.1",
                "gtdb_species": "s__Mycobacterium sp004762045",
                "ani": 87.5508,
                "matched_fragments": 1579,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_001245615.1",
                "gtdb_species": "s__Mycobacterium neworleansense",
                "ani": 86.9602,
                "matched_fragments": 1554,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_002086835.1",
                "gtdb_species": "s__Mycobacterium porcinum",
                "ani": 86.5529,
                "matched_fragments": 1511,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.47",
                "min_intra_species_ani": "97.32",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 9,
                "status": "-"
            },
            {
                "accession": "GCF_001942625.1",
                "gtdb_species": "s__Mycobacterium syngnathidarum",
                "ani": 86.4993,
                "matched_fragments": 1580,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.38",
                "min_intra_species_ani": "97.86",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_001942045.1",
                "gtdb_species": "s__Mycobacterium porcinum_A",
                "ani": 86.496,
                "matched_fragments": 1471,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_000723385.1",
                "gtdb_species": "s__Mycobacterium farcinogenes",
                "ani": 85.9561,
                "matched_fragments": 1511,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.34",
                "min_intra_species_ani": "98.08",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 16,
                "status": "-"
            },
            {
                "accession": "GCF_900078665.2",
                "gtdb_species": "s__Mycobacterium houstonense",
                "ani": 85.4498,
                "matched_fragments": 1471,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_002157835.1",
                "gtdb_species": "s__Mycobacterium dioxanotrophicus",
                "ani": 82.2508,
                "matched_fragments": 1295,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_001905655.1",
                "gtdb_species": "s__Mycobacterium sp001905655",
                "ani": 80.005,
                "matched_fragments": 805,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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_011694515.1",
                "gtdb_species": "s__Mycobacterium sp011694515",
                "ani": 79.3942,
                "matched_fragments": 792,
                "total_fragments": 2114,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium",
                "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": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": null,
        "cell_length": null,
        "doubling_h": null,
        "growth_tmp": null,
        "optimum_tmp": null,
        "optimum_ph": null,
        "genome_size": null,
        "gc_content": null,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": null,
        "sporulation": null,
        "motility": null,
        "range_salinity": null,
        "facultative_respiration": null,
        "anaerobic_respiration": null,
        "aerobic_respiration": null,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "bacillus_cell_shape": null,
        "coccus_cell_shape": null,
        "filament_cell_shape": null,
        "coccobacillus_cell_shape": null,
        "vibrio_cell_shape": null,
        "spiral_cell_shape": null
    },
    "_genome_taxon": [
        "Mycolicibacterium",
        "lutetiense"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}