{
    "type": "genome",
    "identifier": "GCF_003258805.1",
    "organism": "Rhodoplanes elegans",
    "title": "Rhodoplanes elegans",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Indiana University",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_003258805.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN07423869",
        "wgs_master": "NPEU00000000.1",
        "refseq_category": "na",
        "taxid": "29408",
        "species_taxid": "29408",
        "organism_name": "Rhodoplanes elegans",
        "infraspecific_name": "strain=DSM 11907",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2018/06/20",
        "asm_name": "ASM325880v1",
        "asm_submitter": "Indiana University",
        "gbrs_paired_asm": "GCA_003258805.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/258/805/GCF_003258805.1_ASM325880v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "6502640",
        "genome_size_ungapped": "6501370",
        "gc_percent": "69.500000",
        "replicon_count": "0",
        "scaffold_count": "1103",
        "contig_count": "1103",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_003258805.1-RS_2024_03_28",
        "annotation_date": "2024-03-28",
        "total_gene_count": "6423",
        "protein_coding_gene_count": "6051",
        "non_coding_gene_count": "57",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2018-06-20",
    "dateModified": "2018-06-20",
    "datePublished": "2018-06-20",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Rhodoplanes elegans"
        ],
        "sample_taxid": [
            "29408"
        ],
        "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": "1.780 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 95.83,
        "contamination": 4.17,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "6502640",
        "Number of Sequences": "1103",
        "Longest Sequences (bp)": "62976",
        "N50 (bp)": "11051",
        "Gap Ratio (%)": "0.019531",
        "GCcontent (%)": "69.5",
        "Number of CDSs": "5557",
        "Average Protein Length": "295.6",
        "Coding Ratio (%)": "75.8",
        "Number of rRNAs": "3",
        "Number of tRNAs": "58",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Rhodoplanes elegans",
                "strain": "strain=DSM 11907",
                "accession": "GCA_003258805.1",
                "taxid": 29408,
                "species_taxid": 29408,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1649,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Rhodoplanes elegans",
                "strain": "strain=DSM 11907",
                "accession": "GCA_016653355.1",
                "taxid": 29408,
                "species_taxid": 29408,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.8862,
                "matched_fragments": 1607,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Rhodoplanes roseus",
                "strain": "strain=DSM 5909",
                "accession": "GCA_003258865.1",
                "taxid": 29409,
                "species_taxid": 29409,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.6959,
                "matched_fragments": 1160,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodoplanes piscinae",
                "strain": "strain=DSM 19946",
                "accession": "GCA_003258855.1",
                "taxid": 444923,
                "species_taxid": 444923,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.6837,
                "matched_fragments": 937,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodopseudomonas pentothenatexigens",
                "strain": "strain=JA575",
                "accession": "GCA_900218015.1",
                "taxid": 999699,
                "species_taxid": 999699,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.4699,
                "matched_fragments": 550,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bradyrhizobium oropedii",
                "strain": "strain=Pear76",
                "accession": "GCA_020889685.1",
                "taxid": 1571201,
                "species_taxid": 1571201,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.0398,
                "matched_fragments": 492,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bradyrhizobium cajani",
                "strain": "strain=1010",
                "accession": "GCA_009759665.1",
                "taxid": 1928661,
                "species_taxid": 1928661,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.0349,
                "matched_fragments": 536,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bradyrhizobium viridifuturi",
                "strain": "strain=SEMIA 690",
                "accession": "GCA_001238275.1",
                "taxid": 1654716,
                "species_taxid": 1654716,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.973,
                "matched_fragments": 521,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bradyrhizobium quebecense",
                "strain": "strain=66S1MB, /ecotype=symbiovar septentrionalis",
                "accession": "GCA_013373795.3",
                "taxid": 2748629,
                "species_taxid": 2748629,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9362,
                "matched_fragments": 541,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bradyrhizobium elkanii",
                "strain": "strain=USDA 76",
                "accession": "GCA_023278185.1",
                "taxid": 29448,
                "species_taxid": 29448,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9326,
                "matched_fragments": 568,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bradyrhizobium acaciae",
                "strain": "strain=10BB",
                "accession": "GCA_020889785.1",
                "taxid": 2683706,
                "species_taxid": 2683706,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.925,
                "matched_fragments": 515,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bosea thiooxidans",
                "strain": "strain=DSM 9653",
                "accession": "GCA_900168195.1",
                "taxid": 53254,
                "species_taxid": 53254,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.4019,
                "matched_fragments": 432,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Oharaeibacter diazotrophicus",
                "strain": "strain=DSM 102969",
                "accession": "GCA_004362745.1",
                "taxid": 1920512,
                "species_taxid": 1920512,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.2574,
                "matched_fragments": 571,
                "total_fragments": 1671,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.83,
            "contamination": 4.17,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_016653355.1",
                "gtdb_species": "s__Rhodoplanes elegans",
                "ani": 99.8862,
                "matched_fragments": 1607,
                "total_fragments": 1671,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.89",
                "min_intra_species_ani": "99.89",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.96",
                "num_clustered_genomes": 2,
                "status": "conclusive"
            },
            {
                "accession": "GCF_003258865.1",
                "gtdb_species": "s__Rhodoplanes roseus",
                "ani": 86.7088,
                "matched_fragments": 1159,
                "total_fragments": 1671,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes",
                "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": "GCA_013377085.1",
                "gtdb_species": "s__Rhodoplanes sp013377085",
                "ani": 85.653,
                "matched_fragments": 1162,
                "total_fragments": 1671,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes",
                "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": "GCA_009720755.1",
                "gtdb_species": "s__Rhodoplanes serenus",
                "ani": 85.2232,
                "matched_fragments": 1107,
                "total_fragments": 1671,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.72",
                "min_intra_species_ani": "97.48",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_000293785.1",
                "gtdb_species": "s__Rhodoplanes sp000293785",
                "ani": 82.7152,
                "matched_fragments": 869,
                "total_fragments": 1671,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes",
                "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": -0.069,
        "cell_length": 0.389,
        "doubling_h": null,
        "growth_tmp": 26.0,
        "optimum_tmp": 31.666,
        "optimum_ph": 7.25,
        "genome_size": null,
        "gc_content": null,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": 0.0,
        "sporulation": null,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "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": [
        "Rhodoplanes",
        "elegans"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}