{
    "type": "genome",
    "identifier": "GCF_000447205.1",
    "organism": "Sphingobium ummariense RL-3",
    "title": "Sphingobium ummariense RL-3",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "University of Delhi",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000447205.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02471715",
        "wgs_master": "AUWY00000000.1",
        "refseq_category": "reference genome",
        "taxid": "1346791",
        "species_taxid": "420994",
        "organism_name": "Sphingobium ummariense RL-3",
        "infraspecific_name": "strain=RL-3",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2013/08/13",
        "asm_name": "ABySS v1.3.3",
        "asm_submitter": "University of Delhi",
        "gbrs_paired_asm": "GCA_000447205.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/447/205/GCF_000447205.1_ABySS_v1.3.3",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "4754053",
        "genome_size_ungapped": "4754053",
        "gc_percent": "65.000000",
        "replicon_count": "0",
        "scaffold_count": "139",
        "contig_count": "139",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000447205.1-RS_2024_12_11",
        "annotation_date": "2024-12-11",
        "total_gene_count": "4750",
        "protein_coding_gene_count": "4522",
        "non_coding_gene_count": "71",
        "pubmed_id": "24233594"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2013-08-13",
    "dateModified": "2013-08-13",
    "datePublished": "2013-08-13",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Sphingobium ummariense RL-3"
        ],
        "sample_taxid": [
            "1346791"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "1.316 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)": "4754053",
        "Number of Sequences": "139",
        "Longest Sequences (bp)": "249857",
        "N50 (bp)": "87191",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "65.0",
        "Number of CDSs": "4524",
        "Average Protein Length": "305.8",
        "Coding Ratio (%)": "87.3",
        "Number of rRNAs": "12",
        "Number of tRNAs": "57",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Sphingobium ummariense",
                "strain": "strain=RL-3",
                "accession": "GCA_000447205.1",
                "taxid": 420994,
                "species_taxid": 420994,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1497,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Sphingobium indicum",
                "strain": "strain=B90A",
                "accession": "GCA_000264945.2",
                "taxid": 332055,
                "species_taxid": 332055,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.3104,
                "matched_fragments": 770,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium baderi",
                "strain": "strain=LL03",
                "accession": "GCA_000445145.1",
                "taxid": 1332080,
                "species_taxid": 1332080,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.5152,
                "matched_fragments": 660,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium fuliginis",
                "strain": "strain=DSM 18781",
                "accession": "GCA_004152845.1",
                "taxid": 336203,
                "species_taxid": 336203,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.426,
                "matched_fragments": 777,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium baderi",
                "strain": "strain=LL03",
                "accession": "GCA_001046655.1",
                "taxid": 1332080,
                "species_taxid": 1332080,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.3456,
                "matched_fragments": 645,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium fuliginis",
                "strain": "strain=CCM 7327",
                "accession": "GCA_014636045.1",
                "taxid": 336203,
                "species_taxid": 336203,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.3322,
                "matched_fragments": 771,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium cloacae",
                "strain": "strain=JCM 10874",
                "accession": "GCA_002355855.1",
                "taxid": 120107,
                "species_taxid": 120107,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.1551,
                "matched_fragments": 675,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium wenxiniae",
                "strain": "strain=JZ-1",
                "accession": "GCA_014205735.1",
                "taxid": 595605,
                "species_taxid": 595605,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.0733,
                "matched_fragments": 647,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium wenxiniae",
                "strain": "strain=CGMCC 1.7748",
                "accession": "GCA_007830065.1",
                "taxid": 595605,
                "species_taxid": 595605,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.0477,
                "matched_fragments": 652,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium cloacae",
                "strain": "strain=NBRC 102517",
                "accession": "GCA_001591285.1",
                "taxid": 120107,
                "species_taxid": 120107,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.0118,
                "matched_fragments": 653,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium amiense",
                "strain": "strain=DSM 16289",
                "accession": "GCA_003967075.1",
                "taxid": 135719,
                "species_taxid": 135719,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.8205,
                "matched_fragments": 736,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium chungbukense",
                "strain": "strain=DJ77",
                "accession": "GCA_001005725.1",
                "taxid": 56193,
                "species_taxid": 56193,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.5845,
                "matched_fragments": 759,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingobium bisphenolivorans",
                "strain": "strain=YL23",
                "accession": "GCA_000412635.1",
                "taxid": 1335760,
                "species_taxid": 1335760,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.422,
                "matched_fragments": 653,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas changnyeongensis",
                "strain": "strain=C33",
                "accession": "GCA_009913435.1",
                "taxid": 2698679,
                "species_taxid": 2698679,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.539,
                "matched_fragments": 389,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas aracearum",
                "strain": "strain=WZY 27",
                "accession": "GCA_003345355.1",
                "taxid": 2283317,
                "species_taxid": 2283317,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.4561,
                "matched_fragments": 388,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas profundi",
                "strain": "strain=LMO-1",
                "accession": "GCA_009739515.1",
                "taxid": 2681549,
                "species_taxid": 2681549,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.4515,
                "matched_fragments": 441,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas citri",
                "strain": "strain=RRHST34",
                "accession": "GCA_019429485.1",
                "taxid": 2862499,
                "species_taxid": 2862499,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.1982,
                "matched_fragments": 436,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas hylomeconis",
                "strain": "strain=CCTCC AB 2013304",
                "accession": "GCA_025370105.1",
                "taxid": 1395958,
                "species_taxid": 1395958,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.1141,
                "matched_fragments": 381,
                "total_fragments": 1516,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000447205.1",
                "gtdb_species": "s__Sphingobium ummariense",
                "ani": 100.0,
                "matched_fragments": 1496,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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": "conclusive"
            },
            {
                "accession": "GCA_000264945.2",
                "gtdb_species": "s__Sphingobium indicum",
                "ani": 84.3223,
                "matched_fragments": 770,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.64",
                "min_intra_species_ani": "97.75",
                "mean_intra_species_af": "0.82",
                "min_intra_species_af": "0.64",
                "num_clustered_genomes": 8,
                "status": "-"
            },
            {
                "accession": "GCF_001563265.1",
                "gtdb_species": "s__Sphingobium sp001563265",
                "ani": 83.6249,
                "matched_fragments": 800,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.38",
                "min_intra_species_ani": "97.84",
                "mean_intra_species_af": "0.74",
                "min_intra_species_af": "0.68",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_004152845.1",
                "gtdb_species": "s__Sphingobium fuliginis",
                "ani": 83.4109,
                "matched_fragments": 779,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.53",
                "min_intra_species_ani": "97.80",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.78",
                "num_clustered_genomes": 14,
                "status": "-"
            },
            {
                "accession": "GCF_002355855.1",
                "gtdb_species": "s__Sphingobium cloacae",
                "ani": 83.1779,
                "matched_fragments": 671,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "100.00",
                "min_intra_species_ani": "100.00",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_007830065.1",
                "gtdb_species": "s__Sphingobium wenxiniae",
                "ani": 83.0501,
                "matched_fragments": 650,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.17",
                "min_intra_species_ani": "98.76",
                "mean_intra_species_af": "0.86",
                "min_intra_species_af": "0.79",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_003967075.1",
                "gtdb_species": "s__Sphingobium amiense",
                "ani": 82.7965,
                "matched_fragments": 736,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.99",
                "min_intra_species_ani": "99.99",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_002457415.1",
                "gtdb_species": "s__Sphingobium sp002457415",
                "ani": 82.7002,
                "matched_fragments": 656,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_013911745.1",
                "gtdb_species": "s__Sphingobium sp013911745",
                "ani": 82.6145,
                "matched_fragments": 588,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_013375535.1",
                "gtdb_species": "s__Sphingobium sp013375535",
                "ani": 82.5976,
                "matched_fragments": 733,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_001005725.1",
                "gtdb_species": "s__Sphingobium chungbukense",
                "ani": 82.5706,
                "matched_fragments": 761,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.77",
                "min_intra_species_ani": "97.77",
                "mean_intra_species_af": "0.72",
                "min_intra_species_af": "0.72",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_008692605.1",
                "gtdb_species": "s__Sphingobium estronivorans",
                "ani": 82.4426,
                "matched_fragments": 649,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_000412635.1",
                "gtdb_species": "s__Sphingobium bisphenolivorans",
                "ani": 82.4136,
                "matched_fragments": 654,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_900100475.1",
                "gtdb_species": "s__Sphingobium faniae",
                "ani": 82.2696,
                "matched_fragments": 640,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_001456115.1",
                "gtdb_species": "s__Sphingobium baderi_A",
                "ani": 82.2206,
                "matched_fragments": 650,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_014873695.1",
                "gtdb_species": "s__Sphingobium sp014873695",
                "ani": 82.1624,
                "matched_fragments": 738,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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_013375555.1",
                "gtdb_species": "s__Sphingobium sp013375555",
                "ani": 82.1138,
                "matched_fragments": 697,
                "total_fragments": 1516,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium",
                "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": -0.278,
        "cell_length": 0.094,
        "doubling_h": null,
        "growth_tmp": 28.0,
        "optimum_tmp": 28.0,
        "optimum_ph": 7.5,
        "genome_size": 4754053.0,
        "gc_content": 63.812,
        "coding_genes": 4211.023,
        "rRNA16S_genes": 2.333,
        "tRNA_genes": 53.785,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 0.0,
        "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": [
        "Sphingobium",
        "ummariense",
        "RL-3"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}