{
    "type": "genome",
    "identifier": "GCF_011761945.1",
    "organism": "Sphingomonas leidyi",
    "title": "Sphingomonas leidyi",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE Joint Genome Institute",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_011761945.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN12025036",
        "wgs_master": "JAASQV000000000.1",
        "refseq_category": "reference genome",
        "taxid": "68569",
        "species_taxid": "68569",
        "organism_name": "Sphingomonas leidyi",
        "infraspecific_name": "strain=DSM 4733",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2020/03/27",
        "asm_name": "ASM1176194v1",
        "asm_submitter": "DOE Joint Genome Institute",
        "gbrs_paired_asm": "GCA_011761945.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/761/945/GCF_011761945.1_ASM1176194v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "4787838",
        "genome_size_ungapped": "4787742",
        "gc_percent": "67.500000",
        "replicon_count": "0",
        "scaffold_count": "10",
        "contig_count": "10",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_011761945.1-RS_2024_04_19",
        "annotation_date": "2024-04-19",
        "total_gene_count": "4536",
        "protein_coding_gene_count": "4461",
        "non_coding_gene_count": "54",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2020-03-27",
    "dateModified": "2020-03-27",
    "datePublished": "2020-03-27",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Sphingomonas leidyi"
        ],
        "sample_taxid": [
            "68569"
        ],
        "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": "1.298 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)": "4787838",
        "Number of Sequences": "10",
        "Longest Sequences (bp)": "2051387",
        "N50 (bp)": "1221810",
        "Gap Ratio (%)": "0.002005",
        "GCcontent (%)": "67.6",
        "Number of CDSs": "4508",
        "Average Protein Length": "324.7",
        "Coding Ratio (%)": "91.7",
        "Number of rRNAs": "3",
        "Number of tRNAs": "53",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Sphingomonas leidyi",
                "strain": "strain=DSM 4733",
                "accession": "GCA_011761945.1",
                "taxid": 68569,
                "species_taxid": 68569,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1590,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Sphingomonas kyeonggiensis",
                "strain": "strain=DSM 101806",
                "accession": "GCA_014196745.1",
                "taxid": 1268553,
                "species_taxid": 1268553,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.7763,
                "matched_fragments": 1134,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas naasensis",
                "strain": "strain=DSM 100060",
                "accession": "GCA_011762145.1",
                "taxid": 1344951,
                "species_taxid": 1344951,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.0191,
                "matched_fragments": 868,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas naasensis",
                "strain": "strain=KIS18-15",
                "accession": "GCA_004792695.1",
                "taxid": 1344951,
                "species_taxid": 1344951,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.9689,
                "matched_fragments": 870,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas trueperi",
                "strain": "strain=DSM 7225",
                "accession": "GCA_011927635.1",
                "taxid": 53317,
                "species_taxid": 53317,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.4085,
                "matched_fragments": 819,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas pituitosa",
                "strain": "strain=NBRC 102491",
                "accession": "GCA_001598435.1",
                "taxid": 99597,
                "species_taxid": 99597,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.9184,
                "matched_fragments": 764,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas azotifigens",
                "strain": "strain=NBRC 15497",
                "accession": "GCA_002091475.1",
                "taxid": 330920,
                "species_taxid": 330920,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.8077,
                "matched_fragments": 756,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas pokkalii",
                "strain": "strain=L3B27",
                "accession": "GCA_003096275.1",
                "taxid": 2175090,
                "species_taxid": 2175090,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.4951,
                "matched_fragments": 667,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas hengshuiensis",
                "strain": "strain=WHSC-8",
                "accession": "GCA_000935025.1",
                "taxid": 1609977,
                "species_taxid": 1609977,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.4599,
                "matched_fragments": 819,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas psychrotolerans",
                "strain": "strain=Cra20",
                "accession": "GCA_002796605.1",
                "taxid": 1327635,
                "species_taxid": 1327635,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.4082,
                "matched_fragments": 843,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas soli",
                "strain": "strain=NBRC 100801",
                "accession": "GCA_001591025.1",
                "taxid": 266127,
                "species_taxid": 266127,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.1239,
                "matched_fragments": 721,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas koreensis",
                "strain": "strain=NBRC 16723",
                "accession": "GCA_001598395.1",
                "taxid": 93064,
                "species_taxid": 93064,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.5493,
                "matched_fragments": 682,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas koreensis",
                "strain": "strain=JSS26",
                "accession": "GCA_002797435.1",
                "taxid": 93064,
                "species_taxid": 93064,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.5329,
                "matched_fragments": 701,
                "total_fragments": 1591,
                "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": 79.5653,
                "matched_fragments": 591,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas folli",
                "strain": "strain=RHCKR7",
                "accession": "GCA_019429525.1",
                "taxid": 2862497,
                "species_taxid": 2862497,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.515,
                "matched_fragments": 609,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas yunnanensis",
                "strain": "strain=YIM 3",
                "accession": "GCA_019898765.1",
                "taxid": 310400,
                "species_taxid": 310400,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.4099,
                "matched_fragments": 584,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas corticis",
                "strain": "strain=36D10-4-7",
                "accession": "GCA_012035195.1",
                "taxid": 2722791,
                "species_taxid": 2722791,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.0275,
                "matched_fragments": 572,
                "total_fragments": 1591,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_011761945.1",
                "gtdb_species": "s__Sphingomonas leidyi",
                "ani": 100.0,
                "matched_fragments": 1590,
                "total_fragments": 1591,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.87",
                "min_intra_species_ani": "98.83",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 3,
                "status": "conclusive"
            },
            {
                "accession": "GCF_002127225.1",
                "gtdb_species": "s__Sphingomonas sp002127225",
                "ani": 94.6629,
                "matched_fragments": 1312,
                "total_fragments": 1591,
                "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": "GCA_017418975.1",
                "gtdb_species": "s__Sphingomonas sp017418975",
                "ani": 92.5266,
                "matched_fragments": 1298,
                "total_fragments": 1591,
                "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_005503355.1",
                "gtdb_species": "s__Sphingomonas sp005503355",
                "ani": 91.5895,
                "matched_fragments": 1295,
                "total_fragments": 1591,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas",
                "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_014196745.1",
                "gtdb_species": "s__Sphingomonas kyeonggiensis",
                "ani": 87.7918,
                "matched_fragments": 1133,
                "total_fragments": 1591,
                "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_014204495.1",
                "gtdb_species": "s__Sphingomonas kyeonggiensis_A",
                "ani": 87.4978,
                "matched_fragments": 1120,
                "total_fragments": 1591,
                "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_013416555.1",
                "gtdb_species": "s__Sphingomonas sp013416555",
                "ani": 86.9993,
                "matched_fragments": 1071,
                "total_fragments": 1591,
                "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": -0.288,
        "cell_length": 0.14,
        "doubling_h": null,
        "growth_tmp": 30.0,
        "optimum_tmp": 28.407,
        "optimum_ph": 7.016,
        "genome_size": 4164406.103,
        "gc_content": 66.116,
        "coding_genes": 4592.69,
        "rRNA16S_genes": 2.285,
        "tRNA_genes": 51.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 0.586,
        "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": 0.98,
        "coccus_cell_shape": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.019
    },
    "_genome_taxon": [
        "Sphingomonas",
        "leidyi"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}