{
    "type": "genome",
    "identifier": "GCF_900188185.1",
    "organism": "Sphingopyxis indica",
    "title": "Sphingopyxis indica",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE - JOINT GENOME INSTITUTE",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_900188185.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN06295955",
        "wgs_master": "FZPA00000000.1",
        "refseq_category": "na",
        "taxid": "436663",
        "species_taxid": "436663",
        "organism_name": "Sphingopyxis indica",
        "infraspecific_name": "strain=DS15",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2017/07/16",
        "asm_name": "IMG-taxon 2706795027 annotated assembly",
        "asm_submitter": "DOE - JOINT GENOME INSTITUTE",
        "gbrs_paired_asm": "GCA_900188185.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/188/185/GCF_900188185.1_IMG-taxon_2706795027_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": "4149802",
        "genome_size_ungapped": "4149802",
        "gc_percent": "65.500000",
        "replicon_count": "0",
        "scaffold_count": "37",
        "contig_count": "37",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_900188185.1-RS_2024_05_03",
        "annotation_date": "2024-05-03",
        "total_gene_count": "3970",
        "protein_coding_gene_count": "3879",
        "non_coding_gene_count": "52",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2017-07-16",
    "dateModified": "2017-07-16",
    "datePublished": "2017-07-16",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Sphingopyxis indica"
        ],
        "sample_taxid": [
            "436663"
        ],
        "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": "1.134 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)": "4149802",
        "Number of Sequences": "37",
        "Longest Sequences (bp)": "947833",
        "N50 (bp)": "215979",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "65.7",
        "Number of CDSs": "3907",
        "Average Protein Length": "316.7",
        "Coding Ratio (%)": "89.5",
        "Number of rRNAs": "3",
        "Number of tRNAs": "51",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Sphingopyxis indica",
                "strain": "strain=DS15",
                "accession": "GCA_900188185.1",
                "taxid": 436663,
                "species_taxid": 436663,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1361,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Sphingopyxis panaciterrulae",
                "strain": "strain=DSM 27163",
                "accession": "GCA_014199295.1",
                "taxid": 462372,
                "species_taxid": 462372,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.0137,
                "matched_fragments": 856,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis granuli",
                "strain": "strain=NBRC 100800",
                "accession": "GCA_001591045.1",
                "taxid": 267128,
                "species_taxid": 267128,
                "relation_to_type": "type",
                "validated": true,
                "ani": 85.0921,
                "matched_fragments": 739,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis italica",
                "strain": "strain=DSM 25229",
                "accession": "GCA_011926545.1",
                "taxid": 1129133,
                "species_taxid": 1129133,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.5616,
                "matched_fragments": 867,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis terrae subsp. ummariensis",
                "strain": "strain=UI2",
                "accession": "GCA_900177755.1",
                "taxid": 429001,
                "species_taxid": 33052,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.3781,
                "matched_fragments": 773,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis terrae subsp. ummariensis",
                "strain": "strain=DSM 24316",
                "accession": "GCA_002374275.1",
                "taxid": 429001,
                "species_taxid": 33052,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.3592,
                "matched_fragments": 778,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis soli",
                "strain": "strain=BL03",
                "accession": "GCA_018682675.1",
                "taxid": 592051,
                "species_taxid": 592051,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.3354,
                "matched_fragments": 767,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis terrae subsp. terrae",
                "strain": "strain=NBRC 15098",
                "accession": "GCA_001598815.1",
                "taxid": 2448440,
                "species_taxid": 33052,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.1833,
                "matched_fragments": 794,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis macrogoltabida",
                "strain": "strain=203",
                "accession": "GCA_001314325.1",
                "taxid": 33050,
                "species_taxid": 33050,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.1552,
                "matched_fragments": 857,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingopyxis panaciterrae",
                "strain": "strain=DSM 27164",
                "accession": "GCA_011762125.1",
                "taxid": 363841,
                "species_taxid": 363841,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.9362,
                "matched_fragments": 802,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pelagerythrobacter aerophilus",
                "strain": "strain=Ery1",
                "accession": "GCA_003581645.1",
                "taxid": 2306995,
                "species_taxid": 2306995,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.2023,
                "matched_fragments": 376,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas cavernae",
                "strain": "strain=K2R01-6",
                "accession": "GCA_003590775.1",
                "taxid": 2320861,
                "species_taxid": 2320861,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.4797,
                "matched_fragments": 434,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pelagerythrobacter rhizovicinus",
                "strain": "strain=AY-3R",
                "accession": "GCA_004135625.1",
                "taxid": 2268576,
                "species_taxid": 2268576,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.1984,
                "matched_fragments": 341,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Sphingomonas alpina",
                "strain": "strain=DSM 22537",
                "accession": "GCA_025370095.1",
                "taxid": 653931,
                "species_taxid": 653931,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9385,
                "matched_fragments": 410,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Qipengyuania flava",
                "strain": "strain=DSM 16421",
                "accession": "GCA_011762005.1",
                "taxid": 192812,
                "species_taxid": 192812,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.4775,
                "matched_fragments": 274,
                "total_fragments": 1362,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900188185.1",
                "gtdb_species": "s__Sphingopyxis indica",
                "ani": 100.0,
                "matched_fragments": 1361,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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": "GCF_002277025.1",
                "gtdb_species": "s__Sphingopyxis sp002277025",
                "ani": 86.0383,
                "matched_fragments": 874,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_014199295.1",
                "gtdb_species": "s__Sphingopyxis panaciterrulae",
                "ani": 86.0184,
                "matched_fragments": 857,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_900078365.1",
                "gtdb_species": "s__Sphingopyxis sp900078365",
                "ani": 85.2329,
                "matched_fragments": 855,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_001591045.1",
                "gtdb_species": "s__Sphingopyxis granuli",
                "ani": 85.1186,
                "matched_fragments": 736,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.56",
                "min_intra_species_ani": "96.77",
                "mean_intra_species_af": "0.81",
                "min_intra_species_af": "0.78",
                "num_clustered_genomes": 6,
                "status": "-"
            },
            {
                "accession": "GCA_013821905.1",
                "gtdb_species": "s__Sphingopyxis sp013821905",
                "ani": 84.5983,
                "matched_fragments": 664,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_001468285.1",
                "gtdb_species": "s__Sphingopyxis sp001468285",
                "ani": 84.3972,
                "matched_fragments": 828,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.98",
                "min_intra_species_ani": "99.98",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.98",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_018682675.1",
                "gtdb_species": "s__Sphingopyxis soli",
                "ani": 84.3559,
                "matched_fragments": 764,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_001598815.1",
                "gtdb_species": "s__Sphingopyxis terrae",
                "ani": 84.1594,
                "matched_fragments": 796,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.70",
                "min_intra_species_ani": "95.58",
                "mean_intra_species_af": "0.84",
                "min_intra_species_af": "0.76",
                "num_clustered_genomes": 19,
                "status": "-"
            },
            {
                "accession": "GCF_001468395.1",
                "gtdb_species": "s__Sphingopyxis sp001468395",
                "ani": 84.1477,
                "matched_fragments": 817,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.27",
                "min_intra_species_ani": "97.10",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 9,
                "status": "-"
            },
            {
                "accession": "GCF_016734905.1",
                "gtdb_species": "s__Sphingopyxis sp016734905",
                "ani": 84.1243,
                "matched_fragments": 746,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_001314325.1",
                "gtdb_species": "s__Sphingopyxis macrogoltabida",
                "ani": 84.114,
                "matched_fragments": 861,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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": "GCF_001307295.1",
                "gtdb_species": "s__Sphingopyxis macrogoltabida_B",
                "ani": 84.0263,
                "matched_fragments": 846,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_016463645.1",
                "gtdb_species": "s__Sphingopyxis sp016463645",
                "ani": 83.9912,
                "matched_fragments": 754,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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_011762125.1",
                "gtdb_species": "s__Sphingopyxis panaciterrae",
                "ani": 83.9447,
                "matched_fragments": 801,
                "total_fragments": 1362,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis",
                "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": -0.284,
        "cell_length": 0.178,
        "doubling_h": 0.518,
        "growth_tmp": 28.0,
        "optimum_tmp": 28.0,
        "optimum_ph": 7.0,
        "genome_size": 4149802.0,
        "gc_content": 63.768,
        "coding_genes": 4202.933,
        "rRNA16S_genes": 1.0,
        "tRNA_genes": 47.4,
        "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": [
        "Sphingopyxis",
        "indica"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}