{
    "type": "genome",
    "identifier": "GCF_900156265.1",
    "organism": "Acidiphilium rubrum",
    "title": "Acidiphilium rubrum",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE - JOINT GENOME INSTITUTE",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_900156265.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN05421828",
        "wgs_master": "FTNE00000000.1",
        "refseq_category": "reference genome",
        "taxid": "526",
        "species_taxid": "526",
        "organism_name": "Acidiphilium rubrum",
        "infraspecific_name": "strain=ATCC 35905",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2017/01/14",
        "asm_name": "IMG-taxon 2681812815 annotated assembly",
        "asm_submitter": "DOE - JOINT GENOME INSTITUTE",
        "gbrs_paired_asm": "GCA_900156265.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/156/265/GCF_900156265.1_IMG-taxon_2681812815_annotated_assembly",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "3976993",
        "genome_size_ungapped": "3971590",
        "gc_percent": "64.000000",
        "replicon_count": "0",
        "scaffold_count": "78",
        "contig_count": "78",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_900156265.1-RS_2024_12_15",
        "annotation_date": "2024-12-15",
        "total_gene_count": "3812",
        "protein_coding_gene_count": "3709",
        "non_coding_gene_count": "55",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2017-01-14",
    "dateModified": "2017-01-14",
    "datePublished": "2017-01-14",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Acidiphilium rubrum"
        ],
        "sample_taxid": [
            "526"
        ],
        "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": "1.097 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)": "3976993",
        "Number of Sequences": "78",
        "Longest Sequences (bp)": "336326",
        "N50 (bp)": "136338",
        "Gap Ratio (%)": "0.135856",
        "GCcontent (%)": "63.8",
        "Number of CDSs": "3653",
        "Average Protein Length": "323.0",
        "Coding Ratio (%)": "89.0",
        "Number of rRNAs": "3",
        "Number of tRNAs": "49",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Acidiphilium iwatense",
                "strain": "strain=KCTC 23505",
                "accession": "GCA_021556475.1",
                "taxid": 768198,
                "species_taxid": 768198,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.6314,
                "matched_fragments": 572,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Acidiphilium multivorum",
                "strain": "strain=AIU301",
                "accession": "GCA_000202835.1",
                "taxid": 62140,
                "species_taxid": 62140,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.3825,
                "matched_fragments": 558,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Acidiphilium multivorum",
                "strain": "strain=AIU301",
                "accession": "GCA_000964345.1",
                "taxid": 62140,
                "species_taxid": 62140,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.3785,
                "matched_fragments": 497,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Acidocella facilis",
                "strain": "strain=ATCC 35904",
                "accession": "GCA_000687875.1",
                "taxid": 525,
                "species_taxid": 525,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.8917,
                "matched_fragments": 279,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodopila globiformis",
                "strain": "strain=DSM 161",
                "accession": "GCA_002937115.1",
                "taxid": 1071,
                "species_taxid": 1071,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.8527,
                "matched_fragments": 239,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Acidocella aromatica",
                "strain": "strain=DSM 27026",
                "accession": "GCA_014201825.1",
                "taxid": 1303579,
                "species_taxid": 1303579,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.7133,
                "matched_fragments": 199,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Acidisphaera rubrifaciens",
                "strain": "strain=HS-AP3",
                "accession": "GCA_000964365.1",
                "taxid": 50715,
                "species_taxid": 50715,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.7055,
                "matched_fragments": 180,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Acidisoma silvae",
                "strain": "strain=HW T2.11",
                "accession": "GCA_020618775.1",
                "taxid": 2802396,
                "species_taxid": 2802396,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.5311,
                "matched_fragments": 181,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodovastum atsumiense",
                "strain": "strain=G2-11",
                "accession": "GCA_937425535.1",
                "taxid": 504468,
                "species_taxid": 504468,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.4504,
                "matched_fragments": 280,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Roseomonas cervicalis",
                "strain": "strain=ATCC 49957",
                "accession": "GCA_000164635.1",
                "taxid": 204525,
                "species_taxid": 204525,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.3669,
                "matched_fragments": 228,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Roseomonas vastitatis",
                "strain": "strain=CPCC 101021",
                "accession": "GCA_003604215.1",
                "taxid": 2307076,
                "species_taxid": 2307076,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.0945,
                "matched_fragments": 184,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Roseomonas alkaliterrae",
                "strain": "strain=DSM 25895",
                "accession": "GCA_014199195.1",
                "taxid": 1452450,
                "species_taxid": 1452450,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.0264,
                "matched_fragments": 235,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodovarius lipocyclicus",
                "strain": "strain=CCUG 44693",
                "accession": "GCA_009900765.1",
                "taxid": 268410,
                "species_taxid": 268410,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.0059,
                "matched_fragments": 189,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Roseomonas marmotae",
                "strain": "strain=1318",
                "accession": "GCA_017654485.1",
                "taxid": 2768161,
                "species_taxid": 2768161,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.9494,
                "matched_fragments": 185,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodovarius crocodyli",
                "strain": "strain=CCP-6",
                "accession": "GCA_004005855.1",
                "taxid": 1979269,
                "species_taxid": 1979269,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.907,
                "matched_fragments": 185,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Roseococcus microcysteis",
                "strain": "strain=NIBR12",
                "accession": "GCA_014764365.1",
                "taxid": 2771361,
                "species_taxid": 2771361,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.8562,
                "matched_fragments": 172,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pleomorphomonas oryzae",
                "strain": "strain=DSM 16300",
                "accession": "GCA_000422965.1",
                "taxid": 261934,
                "species_taxid": 261934,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.6462,
                "matched_fragments": 81,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas phyllosphaerae",
                "strain": "strain=FA2",
                "accession": "GCA_000427645.1",
                "taxid": 257003,
                "species_taxid": 257003,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.3407,
                "matched_fragments": 113,
                "total_fragments": 1284,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.83,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900156265.1",
                "gtdb_species": "s__Acidiphilium rubrum",
                "ani": 100.0,
                "matched_fragments": 1281,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.80",
                "min_intra_species_ani": "96.68",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.85",
                "num_clustered_genomes": 4,
                "status": "conclusive"
            },
            {
                "accession": "GCF_000202835.1",
                "gtdb_species": "s__Acidiphilium multivorum",
                "ani": 79.3652,
                "matched_fragments": 560,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.69",
                "min_intra_species_ani": "98.42",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 6,
                "status": "-"
            },
            {
                "accession": "GCF_902712915.1",
                "gtdb_species": "s__Acidiphilium sp002255515",
                "ani": 79.1886,
                "matched_fragments": 535,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.59",
                "min_intra_species_ani": "99.19",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_002279355.1",
                "gtdb_species": "s__Acidiphilium sp002279355",
                "ani": 77.6866,
                "matched_fragments": 272,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.80",
                "min_intra_species_ani": "99.77",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_000687875.1",
                "gtdb_species": "s__Acidocella facilis",
                "ani": 76.8836,
                "matched_fragments": 280,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.02",
                "min_intra_species_ani": "98.02",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_002255495.1",
                "gtdb_species": "s__20-60-12 sp002255495",
                "ani": 76.754,
                "matched_fragments": 221,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__20-60-12",
                "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_001899585.1",
                "gtdb_species": "s__70-18 sp001899585",
                "ani": 76.6889,
                "matched_fragments": 295,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.94",
                "min_intra_species_ani": "99.94",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.98",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_003133265.1",
                "gtdb_species": "s__PALSA-911 sp003133265",
                "ani": 76.663,
                "matched_fragments": 199,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911",
                "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_003164135.1",
                "gtdb_species": "s__Acidocella sp003164135",
                "ani": 76.5403,
                "matched_fragments": 207,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.77",
                "min_intra_species_ani": "99.73",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCA_903944925.1",
                "gtdb_species": "s__Rhodopila sp903944925",
                "ani": 76.472,
                "matched_fragments": 195,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.96",
                "min_intra_species_ani": "99.95",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.97",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_903900905.1",
                "gtdb_species": "s__CAIXEA01 sp903900905",
                "ani": 76.3188,
                "matched_fragments": 151,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIXEA01",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.81",
                "min_intra_species_ani": "98.71",
                "mean_intra_species_af": "0.81",
                "min_intra_species_af": "0.80",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_017307285.1",
                "gtdb_species": "s__JAFKFI01 sp017307285",
                "ani": 76.2208,
                "matched_fragments": 224,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01",
                "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_903928045.1",
                "gtdb_species": "s__CAIYPH01 sp903928045",
                "ani": 76.1634,
                "matched_fragments": 171,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIYPH01",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.55",
                "min_intra_species_ani": "98.55",
                "mean_intra_species_af": "0.76",
                "min_intra_species_af": "0.76",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_003604215.1",
                "gtdb_species": "s__Roseomonas vastitatis",
                "ani": 76.0856,
                "matched_fragments": 185,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas",
                "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_902506455.1",
                "gtdb_species": "s__Sphingomonas sp902506455",
                "ani": 75.4927,
                "matched_fragments": 111,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas",
                "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_000427645.1",
                "gtdb_species": "s__Sphingomonas phyllosphaerae",
                "ani": 75.3476,
                "matched_fragments": 112,
                "total_fragments": 1284,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas",
                "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": -0.302,
        "cell_length": 0.176,
        "doubling_h": null,
        "growth_tmp": 20.0,
        "optimum_tmp": 35.0,
        "optimum_ph": null,
        "genome_size": 3976993.0,
        "gc_content": 64.405,
        "coding_genes": 3695.416,
        "rRNA16S_genes": 2.0,
        "tRNA_genes": 48.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": null,
        "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": [
        "Acidiphilium",
        "rubrum"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}