{
    "type": "genome",
    "identifier": "GCA_022548865.1",
    "organism": "Xylella fastidiosa subsp. multiplex",
    "title": "Xylella fastidiosa subsp. multiplex",
    "description": "derived from metagenome",
    "data type": "Genome sequencing and assembly",
    "organization": "USDA-ARS",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCA_022548865.1",
        "bioproject": "PRJNA802263",
        "biosample": "SAMN25524827",
        "wgs_master": "JAKZEN000000000.1",
        "refseq_category": "na",
        "taxid": "644357",
        "species_taxid": "2371",
        "organism_name": "Xylella fastidiosa subsp. multiplex",
        "infraspecific_name": "",
        "isolate": "P5A2",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2022/03/12",
        "asm_name": "ASM2254886v1",
        "submitter": "USDA-ARS",
        "gbrs_paired_asm": "na",
        "paired_asm_comp": "na",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/548/865/GCA_022548865.1_ASM2254886v1",
        "excluded_from_refseq": "derived from metagenome",
        "relation_to_type_material": "",
        "asm_not_live_date": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2022-03-12",
    "dateModified": "2022-03-12",
    "datePublished": "2022-03-12",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Xylella fastidiosa subsp. multiplex"
        ],
        "sample_taxid": [
            "644357"
        ],
        "sample_host_organism": [
            "Prunus persica"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "USA: Alabama"
        ],
        "sample_host_location_id": [],
        "data_size": "0.700 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)": "2461124",
        "Number of Sequences": "51",
        "Longest Sequences (bp)": "273383",
        "N50 (bp)": "136797",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "51.9",
        "Number of CDSs": "2075",
        "Average Protein Length": "305.3",
        "Coding Ratio (%)": "77.2",
        "Number of rRNAs": "6",
        "Number of tRNAs": "49",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Xylella fastidiosa subsp. multiplex",
                "strain": "strain=ATCC 35871",
                "accession": "GCA_000428665.1",
                "taxid": 644357,
                "species_taxid": 2371,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.4815,
                "matched_fragments": 743,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Xylella fastidiosa",
                "strain": "strain=DSM 10026",
                "accession": "GCA_900129695.1",
                "taxid": 2371,
                "species_taxid": 2371,
                "relation_to_type": "type",
                "validated": true,
                "ani": 97.8452,
                "matched_fragments": 726,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Xylella fastidiosa",
                "strain": "strain=ATCC 35879",
                "accession": "GCA_000767565.1",
                "taxid": 2371,
                "species_taxid": 2371,
                "relation_to_type": "type",
                "validated": true,
                "ani": 97.8246,
                "matched_fragments": 754,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Xylella fastidiosa",
                "strain": "strain=ATCC 35879",
                "accession": "GCA_011801475.1",
                "taxid": 2371,
                "species_taxid": 2371,
                "relation_to_type": "type",
                "validated": true,
                "ani": 97.8189,
                "matched_fragments": 759,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Xylella taiwanensis",
                "strain": "strain=PLS229",
                "accession": "GCA_013177435.1",
                "taxid": 1444770,
                "species_taxid": 1444770,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.0295,
                "matched_fragments": 650,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas hydrangeae",
                "strain": "strain=LMG 31884",
                "accession": "GCA_905142475.1",
                "taxid": 2775159,
                "species_taxid": 2775159,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.5147,
                "matched_fragments": 65,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas indica",
                "strain": "strain=PPL560",
                "accession": "GCA_022669045.1",
                "taxid": 2912242,
                "species_taxid": 2912242,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.7903,
                "matched_fragments": 62,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Xanthomonas translucens",
                "strain": "strain=ATCC 19319",
                "accession": "GCA_020880735.1",
                "taxid": 343,
                "species_taxid": 343,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.6004,
                "matched_fragments": 58,
                "total_fragments": 797,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_011801475.1",
                "gtdb_species": "s__Xylella fastidiosa",
                "ani": 97.8168,
                "matched_fragments": 758,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.40",
                "min_intra_species_ani": "96.23",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 130,
                "status": "conclusive"
            },
            {
                "accession": "GCF_013177435.1",
                "gtdb_species": "s__Xylella taiwanensis",
                "ani": 83.0191,
                "matched_fragments": 653,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xylella",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "100.00",
                "min_intra_species_ani": "99.99",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_001700965.1",
                "gtdb_species": "s__Stenotrophomonas nitritireducens_A",
                "ani": 77.3549,
                "matched_fragments": 56,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas",
                "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_905142465.1",
                "gtdb_species": "s__Xanthomonas sp905142465",
                "ani": 77.2753,
                "matched_fragments": 61,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas",
                "ani_circumscription_radius": 95.1927,
                "mean_intra_species_ani": "99.49",
                "min_intra_species_ani": "99.23",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.96",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_012848175.1",
                "gtdb_species": "s__Xanthomonas campestris_C",
                "ani": 77.0837,
                "matched_fragments": 80,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas",
                "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_001908725.1",
                "gtdb_species": "s__Xanthomonas vesicatoria",
                "ani": 76.9114,
                "matched_fragments": 69,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.30",
                "min_intra_species_ani": "98.65",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 15,
                "status": "-"
            },
            {
                "accession": "GCF_001676385.1",
                "gtdb_species": "s__Stenotrophomonas maltophilia_J",
                "ani": 76.7139,
                "matched_fragments": 60,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas",
                "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_000331775.1",
                "gtdb_species": "s__Xanthomonas_A translucens",
                "ani": 76.6814,
                "matched_fragments": 57,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.09",
                "min_intra_species_ani": "95.18",
                "mean_intra_species_af": "0.88",
                "min_intra_species_af": "0.77",
                "num_clustered_genomes": 59,
                "status": "-"
            },
            {
                "accession": "GCF_001431465.1",
                "gtdb_species": "s__Stenotrophomonas terrae",
                "ani": 76.6004,
                "matched_fragments": 60,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas",
                "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_004216795.1",
                "gtdb_species": "s__Stenotrophomonas_A sp004216795",
                "ani": 76.5212,
                "matched_fragments": 56,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_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_002940205.1",
                "gtdb_species": "s__Xanthomonas arboricola_C",
                "ani": 76.5016,
                "matched_fragments": 66,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.99",
                "min_intra_species_ani": "99.99",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_014654535.1",
                "gtdb_species": "s__Pseudomonas_S boreopolis",
                "ani": 76.4613,
                "matched_fragments": 70,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.68",
                "min_intra_species_ani": "98.68",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001431415.1",
                "gtdb_species": "s__Stenotrophomonas humi",
                "ani": 76.2897,
                "matched_fragments": 55,
                "total_fragments": 797,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas",
                "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": -0.699,
        "cell_length": null,
        "doubling_h": 0.707,
        "growth_tmp": 27.633,
        "optimum_tmp": 27.448,
        "optimum_ph": null,
        "genome_size": 2617813.81,
        "gc_content": 51.774,
        "coding_genes": 2296.16,
        "rRNA16S_genes": 2.0,
        "tRNA_genes": 49.647,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": 0.0,
        "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
    },
    "_gtdb_taxon": [
        "d__Bacteria",
        "p__Pseudomonadota",
        "c__Gammaproteobacteria",
        "o__Xanthomonadales",
        "f__Xanthomonadaceae",
        "g__Xylella",
        "s__Xylella fastidiosa"
    ],
    "_genome_taxon": [
        "Xylella",
        "fastidiosa",
        "subsp.",
        "multiplex",
        "d__Bacteria",
        "p__Pseudomonadota",
        "c__Gammaproteobacteria",
        "o__Xanthomonadales",
        "f__Xanthomonadaceae",
        "g__Xylella",
        "s__Xylella fastidiosa",
        "Bacteria",
        "Pseudomonadota",
        "Gammaproteobacteria",
        "Xanthomonadales",
        "Xanthomonadaceae",
        "Xylella",
        "Xylella",
        "fastidiosa"
    ],
    "_meo": [
        {
            "id": "MEO_0000055",
            "label": "rhizosphere"
        }
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}