{
    "type": "genome",
    "identifier": "GCF_000337795.1",
    "organism": "Haloferax denitrificans ATCC 35960",
    "title": "Haloferax denitrificans ATCC 35960",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "University of California, Davis",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000337795.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN02471644",
        "wgs_master": "AOLP00000000.1",
        "refseq_category": "reference genome",
        "taxid": "662478",
        "species_taxid": "35745",
        "organism_name": "Haloferax denitrificans ATCC 35960",
        "infraspecific_name": "strain=ATCC 35960",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2013/02/04",
        "asm_name": "ASM33779v1",
        "asm_submitter": "University of California, Davis",
        "gbrs_paired_asm": "GCA_000337795.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/795/GCF_000337795.1_ASM33779v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "archaea",
        "genome_size": "3825973",
        "genome_size_ungapped": "3825973",
        "gc_percent": "66.500000",
        "replicon_count": "0",
        "scaffold_count": "21",
        "contig_count": "21",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_000337795.1-RS_2024_10_21",
        "annotation_date": "2024-10-21",
        "total_gene_count": "3875",
        "protein_coding_gene_count": "3749",
        "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": [
            "Haloferax denitrificans ATCC 35960"
        ],
        "sample_taxid": [
            "662478"
        ],
        "sample_host_organism": [],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [],
        "sample_host_location_id": [],
        "data_size": "1.035 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 95.83,
        "contamination": 8.33,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "3825973",
        "Number of Sequences": "21",
        "Longest Sequences (bp)": "473491",
        "N50 (bp)": "367032",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "66.3",
        "Number of CDSs": "3814",
        "Average Protein Length": "286.9",
        "Coding Ratio (%)": "85.8",
        "Number of rRNAs": "2",
        "Number of tRNAs": "52",
        "Number of CRISPRs": "6"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Haloferax denitrificans",
                "strain": "strain=ATCC 35960",
                "accession": "GCA_000337795.1",
                "taxid": 35745,
                "species_taxid": 35745,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 1263,
                "total_fragments": 1263,
                "ani_threshold": 95,
                "status": "inconclusive"
            },
            {
                "organism_name": "Haloferax sulfurifontis",
                "strain": "strain=CCM 7217",
                "accession": "GCA_014635105.1",
                "taxid": 255616,
                "species_taxid": 255616,
                "relation_to_type": "type",
                "validated": true,
                "ani": 97.0134,
                "matched_fragments": 1124,
                "total_fragments": 1263,
                "ani_threshold": 95,
                "status": "inconclusive"
            },
            {
                "organism_name": "Haloferax sulfurifontis",
                "strain": "strain=ATCC BAA-897",
                "accession": "GCA_000337835.1",
                "taxid": 255616,
                "species_taxid": 255616,
                "relation_to_type": "type",
                "validated": true,
                "ani": 96.8219,
                "matched_fragments": 1094,
                "total_fragments": 1263,
                "ani_threshold": 95,
                "status": "inconclusive"
            },
            {
                "organism_name": "Haloferax massiliensis",
                "strain": "strain=Arc-Hr",
                "accession": "GCA_001368915.1",
                "taxid": 1476858,
                "species_taxid": 1476858,
                "relation_to_type": "type",
                "validated": true,
                "ani": 94.7758,
                "matched_fragments": 1094,
                "total_fragments": 1263,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Haloferax marisrubri",
                "strain": "strain=SB3",
                "accession": "GCA_001469875.2",
                "taxid": 1544719,
                "species_taxid": 1544719,
                "relation_to_type": "type",
                "validated": true,
                "ani": 94.0646,
                "matched_fragments": 1018,
                "total_fragments": 1263,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Haloferax volcanii",
                "strain": "strain=DS2",
                "accession": "GCA_000337315.1",
                "taxid": 2246,
                "species_taxid": 2246,
                "relation_to_type": "type",
                "validated": true,
                "ani": 94.0364,
                "matched_fragments": 1023,
                "total_fragments": 1263,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.83,
            "contamination": 8.33,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000337795.1",
                "gtdb_species": "s__Haloferax denitrificans",
                "ani": 100.0,
                "matched_fragments": 1263,
                "total_fragments": 1263,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax",
                "ani_circumscription_radius": 96.9285,
                "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_000337835.1",
                "gtdb_species": "s__Haloferax sulfurifontis",
                "ani": 96.8014,
                "matched_fragments": 1095,
                "total_fragments": 1263,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax",
                "ani_circumscription_radius": 96.9285,
                "mean_intra_species_ani": "99.04",
                "min_intra_species_ani": "99.04",
                "mean_intra_species_af": "0.92",
                "min_intra_species_af": "0.92",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001368915.1",
                "gtdb_species": "s__Haloferax massiliensis",
                "ani": 94.8125,
                "matched_fragments": 1091,
                "total_fragments": 1263,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax",
                "ani_circumscription_radius": 95.2845,
                "mean_intra_species_ani": "98.47",
                "min_intra_species_ani": "96.94",
                "mean_intra_species_af": "0.94",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_001469875.2",
                "gtdb_species": "s__Haloferax marisrubri",
                "ani": 94.0646,
                "matched_fragments": 1018,
                "total_fragments": 1263,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "95.85",
                "min_intra_species_ani": "95.85",
                "mean_intra_species_af": "0.83",
                "min_intra_species_af": "0.83",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_000025685.1",
                "gtdb_species": "s__Haloferax volcanii",
                "ani": 93.9397,
                "matched_fragments": 1044,
                "total_fragments": 1263,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.27",
                "min_intra_species_ani": "96.62",
                "mean_intra_species_af": "0.93",
                "min_intra_species_af": "0.89",
                "num_clustered_genomes": 21,
                "status": "-"
            },
            {
                "accession": "GCF_001482285.1",
                "gtdb_species": "s__Haloferax sp001482285",
                "ani": 93.6056,
                "matched_fragments": 1025,
                "total_fragments": 1263,
                "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax",
                "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": -0.097,
        "cell_length": 0.301,
        "doubling_h": 0.264,
        "growth_tmp": 37.0,
        "optimum_tmp": 37.0,
        "optimum_ph": 7.1,
        "genome_size": 3848468.0,
        "gc_content": 62.184,
        "coding_genes": 3795.444,
        "rRNA16S_genes": 2.333,
        "tRNA_genes": 53.666,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "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": 0.666,
        "coccus_cell_shape": 0.333,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 0.0
    },
    "_genome_taxon": [
        "Haloferax",
        "denitrificans",
        "ATCC",
        "35960"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}