{
    "type": "genome",
    "identifier": "GCF_000337095.1",
    "organism": "Halogeometricum pallidum JCM 14848",
    "title": "Halogeometricum pallidum JCM 14848",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "University of California, Davis",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000337095.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02471630",
        "wgs_master": "AOIV00000000.1",
        "refseq_category": "reference genome",
        "taxid": "1227487",
        "species_taxid": "411361",
        "organism_name": "Halogeometricum pallidum JCM 14848",
        "infraspecific_name": "strain=JCM 14848",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2013/02/04",
        "asm_name": "ASM33709v1",
        "asm_submitter": "University of California, Davis",
        "gbrs_paired_asm": "GCA_000337095.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/095/GCF_000337095.1_ASM33709v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "archaea",
        "genome_size": "4384515",
        "genome_size_ungapped": "4384515",
        "gc_percent": "65.500000",
        "replicon_count": "0",
        "scaffold_count": "45",
        "contig_count": "45",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000337095.1-RS_2024_10_21",
        "annotation_date": "2024-10-21",
        "total_gene_count": "4403",
        "protein_coding_gene_count": "4231",
        "non_coding_gene_count": "58",
        "pubmed_id": "25393412"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2013-02-04",
    "dateModified": "2013-02-04",
    "datePublished": "2013-02-04",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Halogeometricum pallidum JCM 14848"
        ],
        "sample_taxid": [
            "1227487"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "1.196 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 95.83,
        "contamination": 4.17,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "4384515",
        "Number of Sequences": "45",
        "Longest Sequences (bp)": "345306",
        "N50 (bp)": "202678",
        "Gap Ratio (%)": "0.002577",
        "GCcontent (%)": "65.6",
        "Number of CDSs": "4266",
        "Average Protein Length": "290.2",
        "Coding Ratio (%)": "84.7",
        "Number of rRNAs": "3",
        "Number of tRNAs": "53",
        "Number of CRISPRs": "3"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Halogeometricum pallidum",
                "strain": "strain=JCM 14848",
                "accession": "GCA_000337095.1",
                "taxid": 411361,
                "species_taxid": 411361,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1439,
                "total_fragments": 1439,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Halogeometricum rufum",
                "strain": "strain=CGMCC 1.7736",
                "accession": "GCA_900112175.1",
                "taxid": 553469,
                "species_taxid": 553469,
                "relation_to_type": "type",
                "validated": true,
                "ani": 85.1261,
                "matched_fragments": 895,
                "total_fragments": 1439,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Halogeometricum limi",
                "strain": "strain=CGMCC 1.8711",
                "accession": "GCA_900115785.1",
                "taxid": 555875,
                "species_taxid": 555875,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.2776,
                "matched_fragments": 850,
                "total_fragments": 1439,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Halogeometricum borinquense",
                "strain": "strain=PR 3",
                "accession": "GCA_000172995.2",
                "taxid": 60847,
                "species_taxid": 60847,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.4108,
                "matched_fragments": 704,
                "total_fragments": 1439,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Halogeometricum borinquense",
                "strain": "strain=DSM 11551",
                "accession": "GCA_000337855.1",
                "taxid": 60847,
                "species_taxid": 60847,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.3273,
                "matched_fragments": 695,
                "total_fragments": 1439,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.83,
            "contamination": 4.17,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000337095.1",
                "gtdb_species": "s__Halogeometricum pallidum",
                "ani": 100.0,
                "matched_fragments": 1439,
                "total_fragments": 1439,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum",
                "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_900112175.1",
                "gtdb_species": "s__Halogeometricum rufum",
                "ani": 85.1547,
                "matched_fragments": 893,
                "total_fragments": 1439,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.26",
                "min_intra_species_ani": "98.26",
                "mean_intra_species_af": "0.87",
                "min_intra_species_af": "0.87",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_900115785.1",
                "gtdb_species": "s__Halogeometricum limi",
                "ani": 84.3009,
                "matched_fragments": 848,
                "total_fragments": 1439,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum",
                "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_900100875.1",
                "gtdb_species": "s__Halopelagius longus",
                "ani": 82.1801,
                "matched_fragments": 744,
                "total_fragments": 1439,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius",
                "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": "-"
            },
            {
                "accession": "GCF_000172995.2",
                "gtdb_species": "s__Halogeometricum borinquense",
                "ani": 81.4018,
                "matched_fragments": 705,
                "total_fragments": 1439,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.42",
                "min_intra_species_ani": "96.84",
                "mean_intra_species_af": "0.96",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 5,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.199,
        "cell_length": -0.199,
        "doubling_h": 0.232,
        "growth_tmp": 43.0,
        "optimum_tmp": 30.0,
        "optimum_ph": 6.5,
        "genome_size": 4384515.0,
        "gc_content": 59.035,
        "coding_genes": 3805.667,
        "rRNA16S_genes": 2.0,
        "tRNA_genes": 53.0,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 0.0,
        "range_salinity": 1.0,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "mesophilic_range_tmp": null,
        "thermophilic_range_tmp": null,
        "psychrophilic_range_tmp": null,
        "bacillus_cell_shape": 0.0,
        "coccus_cell_shape": 1.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.0
    },
    "_genome_taxon": [
        "Halogeometricum",
        "pallidum",
        "JCM",
        "14848"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}