{
    "type": "genome",
    "identifier": "GCF_001311525.1",
    "organism": "Secundilactobacillus oryzae JCM 18671",
    "title": "Secundilactobacillus oryzae JCM 18671",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "The University of Tokyo",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_001311525.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMD00000461",
        "wgs_master": "BBAZ00000000.1",
        "refseq_category": "na",
        "taxid": "1291743",
        "species_taxid": "1202668",
        "organism_name": "Secundilactobacillus oryzae JCM 18671",
        "infraspecific_name": "strain=JCM 18671",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2015/10/01",
        "asm_name": "ASM131152v1",
        "asm_submitter": "The University of Tokyo",
        "gbrs_paired_asm": "GCA_001311525.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/311/525/GCF_001311525.1_ASM131152v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "1840174",
        "genome_size_ungapped": "1840174",
        "gc_percent": "43.000000",
        "replicon_count": "0",
        "scaffold_count": "91",
        "contig_count": "91",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_001311525.1-RS_2024_08_08",
        "annotation_date": "2024-08-08",
        "total_gene_count": "2156",
        "protein_coding_gene_count": "1504",
        "non_coding_gene_count": "66",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2015-10-01",
    "dateModified": "2015-10-01",
    "datePublished": "2015-10-01",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Secundilactobacillus oryzae JCM 18671"
        ],
        "sample_taxid": [
            "1291743"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "missing"
        ],
        "sample_host_location_id": [],
        "data_size": "0.528 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 95.83,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "1840174",
        "Number of Sequences": "91",
        "Longest Sequences (bp)": "155249",
        "N50 (bp)": "47010",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "42.8",
        "Number of CDSs": "2496",
        "Average Protein Length": "206.4",
        "Coding Ratio (%)": "84.0",
        "Number of rRNAs": "2",
        "Number of tRNAs": "56",
        "Number of CRISPRs": "2"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Secundilactobacillus oryzae",
                "strain": "strain=JCM 18671",
                "accession": "GCA_001311525.1",
                "taxid": 1202668,
                "species_taxid": 1202668,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 569,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Secundilactobacillus oryzae",
                "strain": "strain=SG293",
                "accession": "GCA_000740055.1",
                "taxid": 1202668,
                "species_taxid": 1202668,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.8801,
                "matched_fragments": 571,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Secundilactobacillus malefermentans",
                "strain": "strain=ATCC 49373",
                "accession": "GCA_004354735.1",
                "taxid": 176292,
                "species_taxid": 176292,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.5655,
                "matched_fragments": 201,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Secundilactobacillus malefermentans",
                "strain": "strain=DSM 5705",
                "accession": "GCA_001436395.1",
                "taxid": 176292,
                "species_taxid": 176292,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.3268,
                "matched_fragments": 197,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Secundilactobacillus malefermentans",
                "strain": "strain=KCTC 3548",
                "accession": "GCA_000260775.1",
                "taxid": 176292,
                "species_taxid": 176292,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.2864,
                "matched_fragments": 197,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Secundilactobacillus collinoides",
                "strain": "strain=DSM 20515",
                "accession": "GCA_001435975.1",
                "taxid": 33960,
                "species_taxid": 33960,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.8104,
                "matched_fragments": 88,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Secundilactobacillus collinoides",
                "strain": "strain=JCM 1123",
                "accession": "GCA_001312845.1",
                "taxid": 33960,
                "species_taxid": 33960,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.6202,
                "matched_fragments": 85,
                "total_fragments": 572,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.83,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000740055.1",
                "gtdb_species": "s__Secundilactobacillus oryzae",
                "ani": 99.8801,
                "matched_fragments": 571,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.88",
                "min_intra_species_ani": "99.88",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 2,
                "status": "conclusive"
            },
            {
                "accession": "GCF_001311135.1",
                "gtdb_species": "s__Secundilactobacillus paracollinoides",
                "ani": 80.3239,
                "matched_fragments": 79,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.57",
                "min_intra_species_ani": "99.45",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCF_001435575.1",
                "gtdb_species": "s__Lentilactobacillus sunkii",
                "ani": 79.6864,
                "matched_fragments": 57,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.44",
                "min_intra_species_ani": "96.44",
                "mean_intra_species_af": "0.90",
                "min_intra_species_af": "0.90",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_003946265.1",
                "gtdb_species": "s__Levilactobacillus yonginensis",
                "ani": 79.6759,
                "matched_fragments": 80,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus",
                "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_003946245.1",
                "gtdb_species": "s__Levilactobacillus cerevisiae",
                "ani": 79.5949,
                "matched_fragments": 78,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus",
                "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_003946045.1",
                "gtdb_species": "s__Levilactobacillus mulengensis",
                "ani": 79.4684,
                "matched_fragments": 77,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus",
                "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_016861655.1",
                "gtdb_species": "s__Levilactobacillus sp016861655",
                "ani": 79.4094,
                "matched_fragments": 72,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "95.63",
                "min_intra_species_ani": "95.63",
                "mean_intra_species_af": "0.89",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_002583405.1",
                "gtdb_species": "s__Secundilactobacillus silagincola",
                "ani": 79.3896,
                "matched_fragments": 89,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.58",
                "min_intra_species_ani": "97.58",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001436395.1",
                "gtdb_species": "s__Secundilactobacillus malefermentans",
                "ani": 79.3404,
                "matched_fragments": 196,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.75",
                "min_intra_species_ani": "99.27",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 4,
                "status": "-"
            },
            {
                "accession": "GCF_005405185.1",
                "gtdb_species": "s__Secundilactobacillus sp005405185",
                "ani": 79.3194,
                "matched_fragments": 77,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "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_012641075.1",
                "gtdb_species": "s__Secundilactobacillus sp012641075",
                "ani": 79.2574,
                "matched_fragments": 84,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "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_002217925.1",
                "gtdb_species": "s__Secundilactobacillus mixtipabuli",
                "ani": 79.1181,
                "matched_fragments": 86,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "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_001435975.1",
                "gtdb_species": "s__Secundilactobacillus collinoides",
                "ani": 78.8104,
                "matched_fragments": 88,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.82",
                "min_intra_species_ani": "99.79",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.94",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_000785105.2",
                "gtdb_species": "s__Lentilactobacillus curieae",
                "ani": 78.6943,
                "matched_fragments": 56,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus",
                "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_007989105.1",
                "gtdb_species": "s__Lentilactobacillus kefiri",
                "ani": 78.6648,
                "matched_fragments": 67,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.76",
                "min_intra_species_ani": "99.64",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.93",
                "num_clustered_genomes": 9,
                "status": "-"
            },
            {
                "accession": "GCF_016861565.1",
                "gtdb_species": "s__Secundilactobacillus sp016861565",
                "ani": 78.2788,
                "matched_fragments": 70,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus",
                "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_001434785.1",
                "gtdb_species": "s__Levilactobacillus namurensis",
                "ani": 78.0567,
                "matched_fragments": 66,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.48",
                "min_intra_species_ani": "95.39",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 6,
                "status": "-"
            },
            {
                "accession": "GCF_000463075.2",
                "gtdb_species": "s__Lactiplantibacillus plantarum_A",
                "ani": 78.0495,
                "matched_fragments": 51,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.70",
                "min_intra_species_ani": "97.70",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001434055.1",
                "gtdb_species": "s__Levilactobacillus parabrevis",
                "ani": 78.0061,
                "matched_fragments": 57,
                "total_fragments": 572,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.99",
                "min_intra_species_ani": "99.98",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.98",
                "num_clustered_genomes": 3,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": null,
        "cell_length": null,
        "doubling_h": null,
        "growth_tmp": null,
        "optimum_tmp": null,
        "optimum_ph": null,
        "genome_size": null,
        "gc_content": null,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": null,
        "sporulation": null,
        "motility": null,
        "range_salinity": null,
        "facultative_respiration": null,
        "anaerobic_respiration": null,
        "aerobic_respiration": null,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "bacillus_cell_shape": null,
        "coccus_cell_shape": null,
        "filament_cell_shape": null,
        "coccobacillus_cell_shape": null,
        "vibrio_cell_shape": null,
        "spiral_cell_shape": null
    },
    "_genome_taxon": [
        "Secundilactobacillus",
        "oryzae",
        "JCM",
        "18671"
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}