{
    "type": "genome",
    "identifier": "GCF_900104805.1",
    "organism": "Pseudomonas oryzae",
    "title": "Pseudomonas oryzae",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE - JOINT GENOME INSTITUTE",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_900104805.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN05216221",
        "wgs_master": "na",
        "refseq_category": "reference genome",
        "taxid": "1392877",
        "species_taxid": "1392877",
        "organism_name": "Pseudomonas oryzae",
        "infraspecific_name": "strain=KCTC 32247",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Chromosome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2016/10/20",
        "asm_name": "IMG-taxon 2667527434 annotated assembly",
        "asm_submitter": "DOE - JOINT GENOME INSTITUTE",
        "gbrs_paired_asm": "GCA_900104805.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/104/805/GCF_900104805.1_IMG-taxon_2667527434_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": "4642193",
        "genome_size_ungapped": "4642093",
        "gc_percent": "67.500000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_900104805.1-RS_2024_12_11",
        "annotation_date": "2024-12-11",
        "total_gene_count": "4293",
        "protein_coding_gene_count": "4128",
        "non_coding_gene_count": "104",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2016-10-20",
    "dateModified": "2016-10-20",
    "datePublished": "2016-10-20",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Pseudomonas oryzae"
        ],
        "sample_taxid": [
            "1392877"
        ],
        "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": "1.252 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)": "4642093",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "4642093",
        "N50 (bp)": "4642093",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "67.4",
        "Number of CDSs": "4200",
        "Average Protein Length": "327.7",
        "Coding Ratio (%)": "89.0",
        "Number of rRNAs": "21",
        "Number of tRNAs": "87",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Pseudomonas oryzae",
                "strain": "strain=KCTC 32247",
                "accession": "GCA_900104805.1",
                "taxid": 1392877,
                "species_taxid": 1392877,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1545,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Pseudomonas sagittaria",
                "strain": "strain=JCM 18195",
                "accession": "GCA_900115715.1",
                "taxid": 1135990,
                "species_taxid": 1135990,
                "relation_to_type": "type",
                "validated": true,
                "ani": 89.6364,
                "matched_fragments": 1177,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas linyingensis",
                "strain": "strain=LMG 25967",
                "accession": "GCA_900109175.1",
                "taxid": 915471,
                "species_taxid": 915471,
                "relation_to_type": "type",
                "validated": true,
                "ani": 89.1199,
                "matched_fragments": 1142,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas aromaticivorans",
                "strain": "strain=MAP12",
                "accession": "GCA_019097855.1",
                "taxid": 2849492,
                "species_taxid": 2849492,
                "relation_to_type": "type",
                "validated": true,
                "ani": 88.666,
                "matched_fragments": 1065,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas lalucatii",
                "strain": "strain=R1b54",
                "accession": "GCA_018398425.1",
                "taxid": 1424203,
                "species_taxid": 1424203,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.1292,
                "matched_fragments": 824,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Azotobacter chroococcum subsp. isscasi",
                "strain": "strain=P205",
                "accession": "GCA_004327895.1",
                "taxid": 2528971,
                "species_taxid": 353,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.9032,
                "matched_fragments": 831,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Azotobacter chroococcum",
                "strain": "strain=ATCC 9043",
                "accession": "GCA_004327905.1",
                "taxid": 353,
                "species_taxid": 353,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.8731,
                "matched_fragments": 822,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Azotobacter chroococcum",
                "strain": "strain=DSM 2286",
                "accession": "GCA_004339665.1",
                "taxid": 353,
                "species_taxid": 353,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.8556,
                "matched_fragments": 813,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas thermotolerans",
                "strain": "strain=DSM 14292",
                "accession": "GCA_000364625.1",
                "taxid": 157784,
                "species_taxid": 157784,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.7655,
                "matched_fragments": 756,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas jinjuensis",
                "strain": "strain=NBRC 103047",
                "accession": "GCA_002091655.1",
                "taxid": 198616,
                "species_taxid": 198616,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.6955,
                "matched_fragments": 884,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas jinjuensis",
                "strain": "strain=JCM 21621",
                "accession": "GCA_900103845.1",
                "taxid": 198616,
                "species_taxid": 198616,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.6016,
                "matched_fragments": 893,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas insulae",
                "strain": "strain=UL073",
                "accession": "GCA_016901015.1",
                "taxid": 2809017,
                "species_taxid": 2809017,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.0114,
                "matched_fragments": 800,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas cavernae",
                "strain": "strain=K2W31S-8",
                "accession": "GCA_003595175.1",
                "taxid": 2320867,
                "species_taxid": 2320867,
                "relation_to_type": "type",
                "validated": true,
                "ani": 83.006,
                "matched_fragments": 808,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas aeruginosa",
                "strain": "strain=JCM 5962",
                "accession": "GCA_022496575.1",
                "taxid": 287,
                "species_taxid": 287,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.3184,
                "matched_fragments": 835,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Stutzerimonas degradans",
                "strain": "strain=FDAARGOS_876",
                "accession": "GCA_016028635.1",
                "taxid": 2968968,
                "species_taxid": 2968968,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 82.294,
                "matched_fragments": 738,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Pseudomonas indica",
                "strain": "strain=NBRC 103045",
                "accession": "GCA_002091635.1",
                "taxid": 137658,
                "species_taxid": 137658,
                "relation_to_type": "type",
                "validated": true,
                "ani": 82.0228,
                "matched_fragments": 815,
                "total_fragments": 1547,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900104805.1",
                "gtdb_species": "s__Pseudomonas_K oryzae",
                "ani": 100.0,
                "matched_fragments": 1545,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K",
                "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_004801855.1",
                "gtdb_species": "s__Pseudomonas_K sp004801855",
                "ani": 91.2755,
                "matched_fragments": 1054,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.38",
                "min_intra_species_ani": "98.38",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_900115715.1",
                "gtdb_species": "s__Pseudomonas_K sagittaria",
                "ani": 89.6292,
                "matched_fragments": 1177,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K",
                "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_900109175.1",
                "gtdb_species": "s__Pseudomonas_K linyingensis",
                "ani": 89.1145,
                "matched_fragments": 1142,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K",
                "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_019097855.1",
                "gtdb_species": "s__Pseudomonas_K sp019097855",
                "ani": 88.6547,
                "matched_fragments": 1066,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K",
                "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_900105885.1",
                "gtdb_species": "s__Pseudomonas_K guangdongensis",
                "ani": 88.3593,
                "matched_fragments": 859,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.99",
                "min_intra_species_ani": "98.99",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_009363155.1",
                "gtdb_species": "s__Azotobacter salinestris",
                "ani": 83.5147,
                "matched_fragments": 834,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter",
                "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_000380335.1",
                "gtdb_species": "s__Azotobacter vinelandii",
                "ani": 82.9201,
                "matched_fragments": 795,
                "total_fragments": 1547,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.84",
                "min_intra_species_ani": "99.43",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 5,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.248,
        "cell_length": 0.186,
        "doubling_h": -0.025,
        "growth_tmp": 28.767,
        "optimum_tmp": 27.972,
        "optimum_ph": 7.258,
        "genome_size": 4642093.0,
        "gc_content": 60.938,
        "coding_genes": 5204.79,
        "rRNA16S_genes": 5.319,
        "tRNA_genes": 67.35,
        "gram_stain": 0.0,
        "sporulation": 0.013,
        "motility": 0.975,
        "range_salinity": 0.666,
        "facultative_respiration": 0.021,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 0.978,
        "mesophilic_range_tmp": 0.926,
        "thermophilic_range_tmp": 0.0,
        "psychrophilic_range_tmp": 0.073,
        "bacillus_cell_shape": 0.988,
        "coccus_cell_shape": 0.011,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.0
    },
    "_genome_taxon": [
        "Pseudomonas",
        "oryzae"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}