{
    "type": "genome",
    "identifier": "GCF_001646805.1",
    "organism": "Rhodococcus pyridinivorans",
    "title": "Rhodococcus pyridinivorans",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Northumbria University",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_001646805.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN04357314",
        "wgs_master": "LRRI00000000.1",
        "refseq_category": "na",
        "taxid": "103816",
        "species_taxid": "103816",
        "organism_name": "Rhodococcus pyridinivorans",
        "infraspecific_name": "strain=DSM 44555",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2016/05/18",
        "asm_name": "ASM164680v1",
        "asm_submitter": "Northumbria University",
        "gbrs_paired_asm": "GCA_001646805.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/646/805/GCF_001646805.1_ASM164680v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "5181477",
        "genome_size_ungapped": "5181441",
        "gc_percent": "68.000000",
        "replicon_count": "0",
        "scaffold_count": "154",
        "contig_count": "154",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_001646805.1-RS_2024_05_17",
        "annotation_date": "2024-05-17",
        "total_gene_count": "4902",
        "protein_coding_gene_count": "4660",
        "non_coding_gene_count": "60",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2016-05-18",
    "dateModified": "2016-05-18",
    "datePublished": "2016-05-18",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Rhodococcus pyridinivorans"
        ],
        "sample_taxid": [
            "103816"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "missing"
        ],
        "sample_host_location_id": [],
        "data_size": "1.415 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 95.83,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "5181477",
        "Number of Sequences": "154",
        "Longest Sequences (bp)": "204734",
        "N50 (bp)": "89671",
        "Gap Ratio (%)": "0.000695",
        "GCcontent (%)": "67.9",
        "Number of CDSs": "4729",
        "Average Protein Length": "318.9",
        "Coding Ratio (%)": "87.3",
        "Number of rRNAs": "3",
        "Number of tRNAs": "59",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Rhodococcus pyridinivorans",
                "strain": "strain=DSM 44555",
                "accession": "GCA_001646805.1",
                "taxid": 103816,
                "species_taxid": 103816,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1647,
                "total_fragments": 1654,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Rhodococcus pyridinivorans",
                "strain": "strain=DSM 44555",
                "accession": "GCA_900105195.1",
                "taxid": 103816,
                "species_taxid": 103816,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9948,
                "matched_fragments": 1654,
                "total_fragments": 1654,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Rhodococcus pyridinivorans",
                "strain": "strain=NBRC 100608",
                "accession": "GCA_001894905.1",
                "taxid": 103816,
                "species_taxid": 103816,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9777,
                "matched_fragments": 1644,
                "total_fragments": 1654,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Rhodococcus rhodochrous",
                "strain": "strain=DSM 43241",
                "accession": "GCA_001646825.1",
                "taxid": 1829,
                "species_taxid": 1829,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 94.8316,
                "matched_fragments": 1331,
                "total_fragments": 1654,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodococcus rhodochrous",
                "strain": "strain=NCTC10210",
                "accession": "GCA_900187265.1",
                "taxid": 1829,
                "species_taxid": 1829,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 94.7207,
                "matched_fragments": 1367,
                "total_fragments": 1654,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.83,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900105195.1",
                "gtdb_species": "s__Rhodococcus pyridinivorans",
                "ani": 99.9948,
                "matched_fragments": 1654,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.16",
                "min_intra_species_ani": "95.17",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.84",
                "num_clustered_genomes": 21,
                "status": "conclusive"
            },
            {
                "accession": "GCF_900187265.1",
                "gtdb_species": "s__Rhodococcus rhodochrous",
                "ani": 94.7194,
                "matched_fragments": 1367,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.52",
                "min_intra_species_ani": "95.51",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.84",
                "num_clustered_genomes": 11,
                "status": "-"
            },
            {
                "accession": "GCF_001646655.1",
                "gtdb_species": "s__Rhodococcus gordoniae",
                "ani": 91.6546,
                "matched_fragments": 1278,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.98",
                "min_intra_species_ani": "98.16",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_013602415.1",
                "gtdb_species": "s__Rhodococcus sp013602415",
                "ani": 91.1602,
                "matched_fragments": 1411,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "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_015865005.1",
                "gtdb_species": "s__Rhodococcus sp015865005",
                "ani": 81.9921,
                "matched_fragments": 953,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "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_001895025.1",
                "gtdb_species": "s__Rhodococcus zopfii",
                "ani": 81.7099,
                "matched_fragments": 973,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.81",
                "min_intra_species_ani": "97.81",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001646785.1",
                "gtdb_species": "s__Rhodococcus phenolicus",
                "ani": 81.6317,
                "matched_fragments": 929,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "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_012844225.1",
                "gtdb_species": "s__Rhodococcus sp012844225",
                "ani": 81.3633,
                "matched_fragments": 880,
                "total_fragments": 1654,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.09",
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                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 3,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.123,
        "cell_length": 0.518,
        "doubling_h": 0.724,
        "growth_tmp": 30.0,
        "optimum_tmp": 32.333,
        "optimum_ph": 8.0,
        "genome_size": 5177204.818,
        "gc_content": 67.865,
        "coding_genes": 4902.75,
        "rRNA16S_genes": 4.0,
        "tRNA_genes": 54.667,
        "gram_stain": 1.0,
        "sporulation": 0.0,
        "motility": 0.0,
        "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": 1.0,
        "coccus_cell_shape": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.0
    },
    "_genome_taxon": [
        "Rhodococcus",
        "pyridinivorans"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}