{
    "type": "genome",
    "identifier": "GCF_000381785.1",
    "organism": "Amphritea japonica ATCC BAA-1530",
    "title": "Amphritea japonica ATCC BAA-1530",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "DOE Joint Genome Institute",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000381785.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02440491",
        "wgs_master": "ARMN00000000.1",
        "refseq_category": "na",
        "taxid": "1278309",
        "species_taxid": "452627",
        "organism_name": "Amphritea japonica ATCC BAA-1530",
        "infraspecific_name": "strain=JAMM 1866",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2013/04/24",
        "asm_name": "ASM38178v1",
        "asm_submitter": "DOE Joint Genome Institute",
        "gbrs_paired_asm": "GCA_000381785.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/381/785/GCF_000381785.1_ASM38178v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "3799525",
        "genome_size_ungapped": "3796376",
        "gc_percent": "47.500000",
        "replicon_count": "0",
        "scaffold_count": "22",
        "contig_count": "27",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000381785.1-RS_2024_04_26",
        "annotation_date": "2024-04-26",
        "total_gene_count": "3518",
        "protein_coding_gene_count": "3444",
        "non_coding_gene_count": "67",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2013-04-24",
    "dateModified": "2013-04-24",
    "datePublished": "2013-04-24",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Amphritea japonica ATCC BAA-1530"
        ],
        "sample_taxid": [
            "1278309"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Missing"
        ],
        "sample_host_location_id": [],
        "data_size": "1.086 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)": "3799525",
        "Number of Sequences": "22",
        "Longest Sequences (bp)": "893255",
        "N50 (bp)": "572840",
        "Gap Ratio (%)": "0.082879",
        "GCcontent (%)": "47.5",
        "Number of CDSs": "3448",
        "Average Protein Length": "319.1",
        "Coding Ratio (%)": "86.9",
        "Number of rRNAs": "5",
        "Number of tRNAs": "51",
        "Number of CRISPRs": "0"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Amphritea japonica",
                "strain": "strain=JAMM 1866",
                "accession": "GCA_000381785.1",
                "taxid": 452627,
                "species_taxid": 452627,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1255,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Amphritea japonica",
                "strain": "strain=JCM 14782",
                "accession": "GCA_024347275.1",
                "taxid": 452627,
                "species_taxid": 452627,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9952,
                "matched_fragments": 1255,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Amphritea japonica",
                "strain": "strain=ATCC BAA-1530",
                "accession": "GCA_016592435.1",
                "taxid": 452627,
                "species_taxid": 452627,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9929,
                "matched_fragments": 1255,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Amphritea balenae",
                "strain": "strain=JCM 14781",
                "accession": "GCA_014646975.1",
                "taxid": 452629,
                "species_taxid": 452629,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.6185,
                "matched_fragments": 451,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Amphritea balenae",
                "strain": "strain=JAMM 1525",
                "accession": "GCA_003858655.1",
                "taxid": 452629,
                "species_taxid": 452629,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.6095,
                "matched_fragments": 455,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Amphritea atlantica",
                "strain": "strain=DSM 18887",
                "accession": "GCA_900111095.1",
                "taxid": 355243,
                "species_taxid": 355243,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.2865,
                "matched_fragments": 541,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Amphritea pacifica",
                "strain": "strain=ZJ14W",
                "accession": "GCA_016924145.1",
                "taxid": 2811233,
                "species_taxid": 2811233,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.0707,
                "matched_fragments": 529,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Marinobacterium arenosum",
                "strain": "strain=CAU 1594",
                "accession": "GCA_019795155.1",
                "taxid": 2862496,
                "species_taxid": 2862496,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.2846,
                "matched_fragments": 79,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Neptuniibacter pectenicola",
                "strain": "strain=LFT 1.8",
                "accession": "GCA_001597735.1",
                "taxid": 1806669,
                "species_taxid": 1806669,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.0776,
                "matched_fragments": 89,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Marinobacterium alkalitolerans",
                "strain": "strain=AK62",
                "accession": "GCA_017776525.1",
                "taxid": 1542925,
                "species_taxid": 1542925,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.871,
                "matched_fragments": 69,
                "total_fragments": 1255,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_016592435.1",
                "gtdb_species": "s__Amphritea japonica",
                "ani": 99.9929,
                "matched_fragments": 1255,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "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": "conclusive"
            },
            {
                "accession": "GCA_016744155.1",
                "gtdb_species": "s__Amphritea sp016744155",
                "ani": 83.514,
                "matched_fragments": 964,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "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_018067325.1",
                "gtdb_species": "s__Amphritea sp018067325",
                "ani": 83.35,
                "matched_fragments": 652,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.51",
                "min_intra_species_ani": "99.51",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_003858655.1",
                "gtdb_species": "s__Amphritea balenae",
                "ani": 79.5985,
                "matched_fragments": 456,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "100.00",
                "min_intra_species_ani": "100.00",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCA_018223185.1",
                "gtdb_species": "s__Amphritea sp018223185",
                "ani": 79.3059,
                "matched_fragments": 534,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.96",
                "min_intra_species_ani": "99.96",
                "mean_intra_species_af": "0.97",
                "min_intra_species_af": "0.97",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_900111095.1",
                "gtdb_species": "s__Amphritea atlantica",
                "ani": 79.2858,
                "matched_fragments": 541,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "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_018860855.1",
                "gtdb_species": "s__Amphritea atlantica_A",
                "ani": 79.2293,
                "matched_fragments": 389,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "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_016924235.1",
                "gtdb_species": "s__Amphritea sp016924235",
                "ani": 79.2278,
                "matched_fragments": 522,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.30",
                "min_intra_species_ani": "99.30",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001597735.1",
                "gtdb_species": "s__Neptuniibacter pectenicola",
                "ani": 77.0776,
                "matched_fragments": 89,
                "total_fragments": 1255,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.78",
                "min_intra_species_ani": "98.78",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.222,
        "cell_length": -0.046,
        "doubling_h": null,
        "growth_tmp": 20.0,
        "optimum_tmp": 23.0,
        "optimum_ph": 7.125,
        "genome_size": 3799000.5,
        "gc_content": 47.5,
        "coding_genes": null,
        "rRNA16S_genes": null,
        "tRNA_genes": null,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 1.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 0.0,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "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": [
        "Amphritea",
        "japonica",
        "ATCC",
        "BAA-1530"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}