{
    "type": "genome",
    "identifier": "GCF_000092025.1",
    "organism": "Agrobacterium fabrum str. C58",
    "title": "Agrobacterium fabrum str. C58",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Cereon",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000092025.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02603108",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "176299",
        "species_taxid": "1176649",
        "organism_name": "Agrobacterium fabrum str. C58",
        "infraspecific_name": "strain=C58",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2007/11/05",
        "asm_name": "ASM9202v1",
        "asm_submitter": "Cereon",
        "gbrs_paired_asm": "GCA_000092025.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/092/025/GCF_000092025.1_ASM9202v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "5674258",
        "genome_size_ungapped": "5674258",
        "gc_percent": "59.000000",
        "replicon_count": "4",
        "scaffold_count": "4",
        "contig_count": "4",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000092025.1-RS_2024_04_23",
        "annotation_date": "2024-04-23",
        "total_gene_count": "5332",
        "protein_coding_gene_count": "5173",
        "non_coding_gene_count": "71",
        "pubmed_id": "11743194;11743193"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2007-11-05",
    "dateModified": "2007-11-05",
    "datePublished": "2007-11-05",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Agrobacterium fabrum str. C58"
        ],
        "sample_taxid": [
            "176299"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "1.589 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)": "5674258",
        "Number of Sequences": "4",
        "Longest Sequences (bp)": "2841580",
        "N50 (bp)": "2841580",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "59.0",
        "Number of CDSs": "5309",
        "Average Protein Length": "310.4",
        "Coding Ratio (%)": "87.1",
        "Number of rRNAs": "12",
        "Number of tRNAs": "56",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Agrobacterium leguminum",
                "strain": "strain=MOPV5",
                "accession": "GCA_015704895.1",
                "taxid": 2792015,
                "species_taxid": 2792015,
                "relation_to_type": "type",
                "validated": true,
                "ani": 89.3117,
                "matched_fragments": 1418,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Agrobacterium salinitolerans",
                "strain": "strain=YIC 5082",
                "accession": "GCA_002008225.1",
                "taxid": 1183413,
                "species_taxid": 1183413,
                "relation_to_type": "type",
                "validated": true,
                "ani": 89.3016,
                "matched_fragments": 1376,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Agrobacterium tumefaciens",
                "strain": "strain=B6",
                "accession": "GCA_001541315.1",
                "taxid": 358,
                "species_taxid": 358,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 89.1786,
                "matched_fragments": 1459,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Agrobacterium tumefaciens",
                "strain": "strain=B6",
                "accession": "GCA_900045375.1",
                "taxid": 358,
                "species_taxid": 358,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 89.1673,
                "matched_fragments": 1488,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Agrobacterium tumefaciens",
                "strain": "strain=ICMP 5856T",
                "accession": "GCA_009498475.1",
                "taxid": 358,
                "species_taxid": 358,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 89.1659,
                "matched_fragments": 1468,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium oryzihabitans",
                "strain": "strain=M15",
                "accession": "GCA_010669145.1",
                "taxid": 2267833,
                "species_taxid": 2267833,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.8975,
                "matched_fragments": 1371,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhizobium pusense",
                "strain": "strain=LMG 25623",
                "accession": "GCA_900102105.1",
                "taxid": 648995,
                "species_taxid": 648995,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.3913,
                "matched_fragments": 1390,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Shinella sumterensis",
                "strain": "strain=MEC087",
                "accession": "GCA_004514425.2",
                "taxid": 1967501,
                "species_taxid": 1967501,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.0927,
                "matched_fragments": 608,
                "total_fragments": 1889,
                "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": 78.9516,
                "matched_fragments": 683,
                "total_fragments": 1889,
                "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": 78.6078,
                "matched_fragments": 550,
                "total_fragments": 1889,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000092025.1",
                "gtdb_species": "s__Agrobacterium fabrum",
                "ani": 100.0,
                "matched_fragments": 1887,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.52",
                "min_intra_species_ani": "95.41",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.85",
                "num_clustered_genomes": 28,
                "status": "conclusive"
            },
            {
                "accession": "GCF_005221325.1",
                "gtdb_species": "s__Agrobacterium sp900012625",
                "ani": 92.1662,
                "matched_fragments": 1546,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.19",
                "min_intra_species_ani": "97.65",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_017744915.1",
                "gtdb_species": "s__Agrobacterium tumefaciens_I",
                "ani": 90.9251,
                "matched_fragments": 1411,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "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_002008225.1",
                "gtdb_species": "s__Agrobacterium salinitolerans",
                "ani": 89.2908,
                "matched_fragments": 1377,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.86",
                "min_intra_species_ani": "95.71",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 11,
                "status": "-"
            },
            {
                "accession": "GCF_001541315.1",
                "gtdb_species": "s__Agrobacterium tumefaciens",
                "ani": 89.1786,
                "matched_fragments": 1459,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.87",
                "min_intra_species_ani": "95.73",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.83",
                "num_clustered_genomes": 248,
                "status": "-"
            },
            {
                "accession": "GCF_002943835.1",
                "gtdb_species": "s__Agrobacterium deltaense",
                "ani": 89.0862,
                "matched_fragments": 1448,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.62",
                "min_intra_species_ani": "95.20",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.77",
                "num_clustered_genomes": 64,
                "status": "-"
            },
            {
                "accession": "GCF_002005205.3",
                "gtdb_species": "s__Agrobacterium rhizogenes_A",
                "ani": 88.9523,
                "matched_fragments": 1410,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.60",
                "min_intra_species_ani": "97.88",
                "mean_intra_species_af": "0.94",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 11,
                "status": "-"
            },
            {
                "accession": "GCF_005221385.1",
                "gtdb_species": "s__Agrobacterium sp900013535",
                "ani": 88.6231,
                "matched_fragments": 1409,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.00",
                "min_intra_species_ani": "98.18",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 7,
                "status": "-"
            },
            {
                "accession": "GCF_007002745.1",
                "gtdb_species": "s__Agrobacterium rhizogenes_B",
                "ani": 88.5536,
                "matched_fragments": 1423,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "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_013337285.1",
                "gtdb_species": "s__Agrobacterium tumefaciens_H",
                "ani": 88.469,
                "matched_fragments": 1397,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.07",
                "min_intra_species_ani": "97.88",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_000949895.1",
                "gtdb_species": "s__Agrobacterium arsenijevicii",
                "ani": 88.1231,
                "matched_fragments": 1422,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "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_010669145.1",
                "gtdb_species": "s__Agrobacterium oryzihabitans",
                "ani": 87.9135,
                "matched_fragments": 1373,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.96",
                "min_intra_species_ani": "97.17",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.79",
                "num_clustered_genomes": 9,
                "status": "-"
            },
            {
                "accession": "GCF_000949865.1",
                "gtdb_species": "s__Agrobacterium nepotum",
                "ani": 87.5032,
                "matched_fragments": 1360,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "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_009649785.1",
                "gtdb_species": "s__Agrobacterium fabacearum",
                "ani": 87.1929,
                "matched_fragments": 1449,
                "total_fragments": 1889,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.40",
                "min_intra_species_ani": "96.96",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.76",
                "num_clustered_genomes": 243,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": null,
        "cell_length": null,
        "doubling_h": 0.322,
        "growth_tmp": 27.25,
        "optimum_tmp": 26.5,
        "optimum_ph": null,
        "genome_size": 5674219.6,
        "gc_content": 58.015,
        "coding_genes": 5355.0,
        "rRNA16S_genes": 4.0,
        "tRNA_genes": 56.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": 0.5,
        "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": [
        "Agrobacterium",
        "fabrum",
        "str.",
        "C58"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}