{
    "type": "genome",
    "identifier": "GCF_007002985.1",
    "organism": "Rhizobium rhizogenes",
    "title": "Rhizobium rhizogenes",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Institute for Agricultural and Fisheries and Food Research (ILVO)",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_007002985.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN10888982",
        "wgs_master": "SGOG00000000.1",
        "refseq_category": "na",
        "taxid": "359",
        "species_taxid": "359",
        "organism_name": "Rhizobium rhizogenes",
        "infraspecific_name": "strain=LMG150",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2019/07/15",
        "asm_name": "ASM700298v1",
        "asm_submitter": "Institute for Agricultural and Fisheries and Food Research (ILVO)",
        "gbrs_paired_asm": "GCA_007002985.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/002/985/GCF_007002985.1_ASM700298v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "7054120",
        "genome_size_ungapped": "7054120",
        "gc_percent": "60.000000",
        "replicon_count": "0",
        "scaffold_count": "72",
        "contig_count": "72",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_007002985.1-RS_2024_09_13",
        "annotation_date": "2024-09-13",
        "total_gene_count": "6708",
        "protein_coding_gene_count": "6553",
        "non_coding_gene_count": "61",
        "pubmed_id": "31273398"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2019-07-15",
    "dateModified": "2019-07-15",
    "datePublished": "2019-07-15",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Rhizobium rhizogenes"
        ],
        "sample_taxid": [
            "359"
        ],
        "sample_host_organism": [
            "not collected"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "unknown"
        ],
        "sample_host_location_id": [],
        "data_size": "1.978 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 100.0,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "7054120",
        "Number of Sequences": "72",
        "Longest Sequences (bp)": "814679",
        "N50 (bp)": "423091",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "59.9",
        "Number of CDSs": "6684",
        "Average Protein Length": "307.0",
        "Coding Ratio (%)": "87.3",
        "Number of rRNAs": "3",
        "Number of tRNAs": "55",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Agrobacterium rhizogenes",
                "strain": "strain=LMG150",
                "accession": "GCA_007002985.1",
                "taxid": 359,
                "species_taxid": 359,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 2317,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Agrobacterium rhizogenes",
                "strain": "strain=NBRC 13257",
                "accession": "GCA_000696095.1",
                "taxid": 359,
                "species_taxid": 359,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9946,
                "matched_fragments": 2303,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Rhizobium leucaenae",
                "strain": "strain=CFN 299",
                "accession": "GCA_014727215.1",
                "taxid": 29450,
                "species_taxid": 29450,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.9566,
                "matched_fragments": 1306,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium leucaenae",
                "strain": "strain=USDA 9039",
                "accession": "GCA_000426285.1",
                "taxid": 29450,
                "species_taxid": 29450,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.9132,
                "matched_fragments": 1310,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium jaguaris",
                "strain": "strain=CCGE525",
                "accession": "GCA_003627755.1",
                "taxid": 1312183,
                "species_taxid": 1312183,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.9128,
                "matched_fragments": 1380,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium lusitanum",
                "strain": "strain=P1-7",
                "accession": "GCA_900094565.1",
                "taxid": 293958,
                "species_taxid": 293958,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 84.508,
                "matched_fragments": 1440,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium freirei",
                "strain": "strain=PRF 81",
                "accession": "GCA_000359745.1",
                "taxid": 1353277,
                "species_taxid": 1353277,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.5725,
                "matched_fragments": 1265,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium multihospitium",
                "strain": "strain=HAMBI 2975",
                "accession": "GCA_900094585.1",
                "taxid": 410764,
                "species_taxid": 410764,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.479,
                "matched_fragments": 1374,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium miluonense",
                "strain": "strain=HAMBI 2971",
                "accession": "GCA_900094545.1",
                "taxid": 411945,
                "species_taxid": 411945,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.4758,
                "matched_fragments": 1268,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium tropici",
                "strain": "strain=CIAT 899",
                "accession": "GCA_000330885.1",
                "taxid": 398,
                "species_taxid": 398,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.3848,
                "matched_fragments": 1302,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium dioscoreae",
                "strain": "strain=S-93",
                "accession": "GCA_009176305.1",
                "taxid": 2653122,
                "species_taxid": 2653122,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.1991,
                "matched_fragments": 1362,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium croatiense",
                "strain": "strain=13T",
                "accession": "GCA_019793465.1",
                "taxid": 2867516,
                "species_taxid": 2867516,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.0241,
                "matched_fragments": 1023,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium redzepovicii",
                "strain": "strain=18T",
                "accession": "GCA_019793435.1",
                "taxid": 2867518,
                "species_taxid": 2867518,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.9112,
                "matched_fragments": 1053,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium mongolense subsp. loessense",
                "strain": "strain=CGMCC 1.3401",
                "accession": "GCA_900099775.1",
                "taxid": 158890,
                "species_taxid": 57676,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.8754,
                "matched_fragments": 928,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shinella pollutisoli",
                "strain": "strain=KCTC 52677",
                "accession": "GCA_024609765.1",
                "taxid": 2250594,
                "species_taxid": 2250594,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.6684,
                "matched_fragments": 690,
                "total_fragments": 2322,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000696095.1",
                "gtdb_species": "s__Rhizobium rhizogenes",
                "ani": 99.9946,
                "matched_fragments": 2303,
                "total_fragments": 2322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.11",
                "min_intra_species_ani": "97.39",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 92,
                "status": "conclusive"
            },
            {
                "accession": "GCF_009498525.1",
                "gtdb_species": "s__Rhizobium sp009498525",
                "ani": 92.3332,
                "matched_fragments": 1916,
                "total_fragments": 2322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium",
                "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_000799715.1",
                "gtdb_species": "s__Rhizobium rhizogenes_C",
                "ani": 91.3472,
                "matched_fragments": 1760,
                "total_fragments": 2322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium",
                "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_014189535.1",
                "gtdb_species": "s__Rhizobium lusitanum_C",
                "ani": 91.2462,
                "matched_fragments": 1778,
                "total_fragments": 2322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium",
                "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_014195095.1",
                "gtdb_species": "s__Rhizobium sp014195095",
                "ani": 86.7694,
                "matched_fragments": 1628,
                "total_fragments": 2322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium",
                "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_900094565.1",
                "gtdb_species": "s__Rhizobium lusitanum",
                "ani": 84.4834,
                "matched_fragments": 1444,
                "total_fragments": 2322,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.73",
                "min_intra_species_ani": "98.48",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.84",
                "num_clustered_genomes": 20,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.23,
        "cell_length": 0.207,
        "doubling_h": 0.225,
        "growth_tmp": 28.733,
        "optimum_tmp": 28.423,
        "optimum_ph": 6.983,
        "genome_size": 6239444.624,
        "gc_content": 60.147,
        "coding_genes": 6587.615,
        "rRNA16S_genes": 3.0,
        "tRNA_genes": 51.725,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 0.793,
        "range_salinity": null,
        "facultative_respiration": 0.05,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 0.95,
        "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": [
        "Rhizobium",
        "rhizogenes"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}