{
    "type": "genome",
    "identifier": "GCA_001899855.1",
    "organism": "Xanthomonadales bacterium 63-13",
    "title": "Xanthomonadales bacterium 63-13",
    "description": "derived from metagenome; genus undefined",
    "data type": "Genome sequencing and assembly",
    "organization": "Banfield Lab, University of California, Berkeley",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCA_001899855.1",
        "bioproject": "PRJNA279279",
        "biosample": "SAMN05660638",
        "wgs_master": "MKWR00000000.1",
        "refseq_category": "na",
        "taxid": "1895867",
        "species_taxid": "1895867",
        "organism_name": "Xanthomonadales bacterium 63-13",
        "infraspecific_name": "",
        "isolate": "63-13",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2016/12/09",
        "asm_name": "ASM189985v1",
        "submitter": "Banfield Lab, University of California, Berkeley",
        "gbrs_paired_asm": "na",
        "paired_asm_comp": "na",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/899/855/GCA_001899855.1_ASM189985v1",
        "excluded_from_refseq": "derived from metagenome; genus undefined",
        "relation_to_type_material": "",
        "asm_not_live_date": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2016-12-09",
    "dateModified": "2016-12-09",
    "datePublished": "2016-12-09",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Xanthomonadales bacterium 63-13"
        ],
        "sample_taxid": [
            "1895867"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "South Africa: University of Cape Town"
        ],
        "sample_host_location_id": [],
        "data_size": "1.036 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": "MAG",
    "data_source": "INSDC",
    "_dfast": {
        "Total Sequence Length (bp)": "3747714",
        "Number of Sequences": "36",
        "Longest Sequences (bp)": "365109",
        "N50 (bp)": "231928",
        "Gap Ratio (%)": "0.005950",
        "GCcontent (%)": "63.4",
        "Number of CDSs": "3259",
        "Average Protein Length": "341.5",
        "Coding Ratio (%)": "89.1",
        "Number of rRNAs": "1",
        "Number of tRNAs": "43",
        "Number of CRISPRs": "3"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Dokdonella immobilis",
                "strain": "strain=CGMCC 1.7659",
                "accession": "GCA_900115085.1",
                "taxid": 578942,
                "species_taxid": 578942,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.262,
                "matched_fragments": 732,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Dokdonella koreensis",
                "strain": "strain=DS-123",
                "accession": "GCA_001632775.1",
                "taxid": 323415,
                "species_taxid": 323415,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.8119,
                "matched_fragments": 443,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Dokdonella fugitiva",
                "strain": "strain=A3",
                "accession": "GCA_004342425.1",
                "taxid": 328517,
                "species_taxid": 328517,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.3914,
                "matched_fragments": 437,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodanobacter spathiphylli",
                "strain": "strain=B39",
                "accession": "GCA_000264295.1",
                "taxid": 347483,
                "species_taxid": 347483,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.0023,
                "matched_fragments": 340,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Tahibacter caeni",
                "strain": "strain=BUT-6",
                "accession": "GCA_024609805.1",
                "taxid": 1453545,
                "species_taxid": 1453545,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.9064,
                "matched_fragments": 391,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rhodanobacter denitrificans",
                "strain": "strain=2APBS1",
                "accession": "GCA_000230695.3",
                "taxid": 666685,
                "species_taxid": 666685,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.8362,
                "matched_fragments": 342,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Oleiagrimonas soli",
                "strain": "strain=3.5X",
                "accession": "GCA_000761445.1",
                "taxid": 1543381,
                "species_taxid": 1543381,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.7033,
                "matched_fragments": 286,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Frateuria terrea",
                "strain": "strain=CGMCC 1.7053",
                "accession": "GCA_900115705.1",
                "taxid": 529704,
                "species_taxid": 529704,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.6741,
                "matched_fragments": 292,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Fulvimonas soli",
                "strain": "strain=DSM 14263",
                "accession": "GCA_003148905.1",
                "taxid": 155197,
                "species_taxid": 155197,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.6677,
                "matched_fragments": 335,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas sacchari",
                "strain": "strain=CFBP4641",
                "accession": "GCA_002940085.1",
                "taxid": 56458,
                "species_taxid": 56458,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 77.6308,
                "matched_fragments": 275,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Dyella japonica",
                "strain": "strain=DSM 16301",
                "accession": "GCA_001010355.1",
                "taxid": 231455,
                "species_taxid": 231455,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.6178,
                "matched_fragments": 231,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Fulvimonas soli",
                "strain": "strain=LMG 19981",
                "accession": "GCA_006352285.1",
                "taxid": 155197,
                "species_taxid": 155197,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.613,
                "matched_fragments": 323,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Lysobacter arseniciresistens",
                "strain": "strain=ZS79",
                "accession": "GCA_000768335.1",
                "taxid": 1385522,
                "species_taxid": 1385522,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.5878,
                "matched_fragments": 257,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Frateuria flava",
                "strain": "strain=MAH-13",
                "accession": "GCA_017837635.1",
                "taxid": 2821489,
                "species_taxid": 2821489,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.5512,
                "matched_fragments": 285,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Rudaea cellulosilytica",
                "strain": "strain=DSM 22992",
                "accession": "GCA_000378125.1",
                "taxid": 540746,
                "species_taxid": 540746,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.5139,
                "matched_fragments": 337,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Luteimonas lumbrici",
                "strain": "strain=1.1416",
                "accession": "GCA_006476065.1",
                "taxid": 2559601,
                "species_taxid": 2559601,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.4919,
                "matched_fragments": 233,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Oleiagrimonas citrea",
                "strain": "strain=MEBiC09124",
                "accession": "GCA_012395255.1",
                "taxid": 1665687,
                "species_taxid": 1665687,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.4808,
                "matched_fragments": 267,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Lysobacter capsici",
                "strain": "strain=VKM B-2533",
                "accession": "GCA_014779555.2",
                "taxid": 435897,
                "species_taxid": 435897,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.3085,
                "matched_fragments": 312,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas citri",
                "strain": "strain=CFBP 2913",
                "accession": "GCA_002688625.1",
                "taxid": 346,
                "species_taxid": 346,
                "relation_to_type": "pathovar",
                "validated": true,
                "ani": 77.2536,
                "matched_fragments": 225,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas citri",
                "strain": "strain=CFBP7112",
                "accession": "GCA_002218265.1",
                "taxid": 346,
                "species_taxid": 346,
                "relation_to_type": "pathovar",
                "validated": true,
                "ani": 77.2332,
                "matched_fragments": 219,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Dyella mobilis",
                "strain": "strain=DHON07",
                "accession": "GCA_016904945.1",
                "taxid": 1849582,
                "species_taxid": 1849582,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.1776,
                "matched_fragments": 244,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas citri",
                "strain": "strain=LMG867",
                "accession": "GCA_020011255.1",
                "taxid": 346,
                "species_taxid": 346,
                "relation_to_type": "pathovar",
                "validated": true,
                "ani": 77.0436,
                "matched_fragments": 216,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudolysobacter antarcticus",
                "strain": "strain=AQ6-296",
                "accession": "GCA_004168365.1",
                "taxid": 2511995,
                "species_taxid": 2511995,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.009,
                "matched_fragments": 223,
                "total_fragments": 1229,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCA_001899855.1",
                "gtdb_species": "s__Dokdonella sp001899855",
                "ani": 100.0,
                "matched_fragments": 1226,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "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_016707485.1",
                "gtdb_species": "s__Dokdonella sp016707485",
                "ani": 93.4985,
                "matched_fragments": 1003,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.34",
                "min_intra_species_ani": "99.18",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCA_016721015.1",
                "gtdb_species": "s__Dokdonella sp016721015",
                "ani": 82.7981,
                "matched_fragments": 840,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "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_900115085.1",
                "gtdb_species": "s__Dokdonella immobilis",
                "ani": 81.2595,
                "matched_fragments": 733,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "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_016712865.1",
                "gtdb_species": "s__Dokdonella sp016712865",
                "ani": 80.0634,
                "matched_fragments": 570,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.46",
                "min_intra_species_ani": "99.45",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.98",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCA_017302215.1",
                "gtdb_species": "s__Dokdonella sp017302215",
                "ani": 79.7957,
                "matched_fragments": 499,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "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_004295005.1",
                "gtdb_species": "s__Dokdonella sp004295005",
                "ani": 79.4969,
                "matched_fragments": 487,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella",
                "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_009996615.1",
                "gtdb_species": "s__Dokdonella_A sp009996615",
                "ani": 78.6037,
                "matched_fragments": 477,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A",
                "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_004143945.1",
                "gtdb_species": "s__Dokdonella_A sp004143945",
                "ani": 78.4271,
                "matched_fragments": 394,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A",
                "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_000953855.2",
                "gtdb_species": "s__Mizugakiibacter sediminis",
                "ani": 78.311,
                "matched_fragments": 383,
                "total_fragments": 1229,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter",
                "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": -0.355,
        "cell_length": 0.227,
        "doubling_h": 0.355,
        "growth_tmp": 29.562,
        "optimum_tmp": 29.59,
        "optimum_ph": 7.131,
        "genome_size": 4164088.144,
        "gc_content": 65.291,
        "coding_genes": 3964.768,
        "rRNA16S_genes": 2.188,
        "tRNA_genes": 55.224,
        "gram_stain": 0.007,
        "sporulation": 0.0,
        "motility": 0.612,
        "range_salinity": 0.25,
        "facultative_respiration": 0.044,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 0.955,
        "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": 0.009,
        "vibrio_cell_shape": 0.009,
        "spiral_cell_shape": 0.0
    },
    "_gtdb_taxon": [
        "d__Bacteria",
        "p__Pseudomonadota",
        "c__Gammaproteobacteria",
        "o__Xanthomonadales",
        "f__Rhodanobacteraceae",
        "g__Dokdonella",
        "s__Dokdonella sp001899855"
    ],
    "_genome_taxon": [
        "Xanthomonadales",
        "bacterium",
        "63-13",
        "d__Bacteria",
        "p__Pseudomonadota",
        "c__Gammaproteobacteria",
        "o__Xanthomonadales",
        "f__Rhodanobacteraceae",
        "g__Dokdonella",
        "s__Dokdonella sp001899855",
        "Bacteria",
        "Pseudomonadota",
        "Gammaproteobacteria",
        "Xanthomonadales",
        "Rhodanobacteraceae",
        "Dokdonella",
        "Dokdonella",
        "sp001899855"
    ],
    "_meo": [
        {
            "id": "MEO_0000119",
            "label": "bioreactor"
        }
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}