{
    "type": "genome",
    "identifier": "GCF_000765805.2",
    "organism": "Helicobacter muridarum",
    "title": "Helicobacter muridarum",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Massachusetts Institute of Technology",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_000765805.2",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN03075563",
        "wgs_master": "JRPD00000000.2",
        "refseq_category": "na",
        "taxid": "216",
        "species_taxid": "216",
        "organism_name": "Helicobacter muridarum",
        "infraspecific_name": "strain=ST1",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2019/05/22",
        "asm_name": "ASM76580v2",
        "asm_submitter": "Massachusetts Institute of Technology",
        "gbrs_paired_asm": "GCA_000765805.2",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/765/805/GCF_000765805.2_ASM76580v2",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2225182",
        "genome_size_ungapped": "2225182",
        "gc_percent": "32.500000",
        "replicon_count": "0",
        "scaffold_count": "76",
        "contig_count": "76",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)",
        "annotation_date": "2024-01-29",
        "total_gene_count": "2000",
        "protein_coding_gene_count": "1896",
        "non_coding_gene_count": "42",
        "pubmed_id": "25428971"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2019-05-22",
    "dateModified": "2019-05-22",
    "datePublished": "2019-05-22",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Helicobacter muridarum"
        ],
        "sample_taxid": [
            "216"
        ],
        "sample_host_organism": [
            "mouse"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Australia"
        ],
        "sample_host_location_id": [],
        "data_size": "0.619 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)": "2225182",
        "Number of Sequences": "76",
        "Longest Sequences (bp)": "217728",
        "N50 (bp)": "80379",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "32.6",
        "Number of CDSs": "1909",
        "Average Protein Length": "321.9",
        "Coding Ratio (%)": "82.8",
        "Number of rRNAs": "2",
        "Number of tRNAs": "36",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Helicobacter muridarum",
                "strain": "strain=ST1",
                "accession": "GCA_000765805.2",
                "taxid": 216,
                "species_taxid": 216,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 705,
                "total_fragments": 707,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Helicobacter muridarum",
                "strain": "strain=NCTC12714",
                "accession": "GCA_900450885.1",
                "taxid": 216,
                "species_taxid": 216,
                "relation_to_type": "type",
                "validated": true,
                "ani": 99.9954,
                "matched_fragments": 706,
                "total_fragments": 707,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Helicobacter japonicus",
                "strain": "strain=MIT 01-6451",
                "accession": "GCA_000762845.2",
                "taxid": 425400,
                "species_taxid": 425400,
                "relation_to_type": "type",
                "validated": true,
                "ani": 80.2406,
                "matched_fragments": 53,
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                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Helicobacter aurati",
                "strain": "strain=MIT 97-5075",
                "accession": "GCA_003364265.1",
                "taxid": 137778,
                "species_taxid": 137778,
                "relation_to_type": "type",
                "validated": true,
                "ani": 77.5705,
                "matched_fragments": 189,
                "total_fragments": 707,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Helicobacter trogontum",
                "strain": "strain=ATCC 700114",
                "accession": "GCA_000765905.2",
                "taxid": 50960,
                "species_taxid": 50960,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.9594,
                "matched_fragments": 71,
                "total_fragments": 707,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Helicobacter saguini",
                "strain": "strain=MIT 97-6194",
                "accession": "GCA_000762875.2",
                "taxid": 1548018,
                "species_taxid": 1548018,
                "relation_to_type": "type",
                "validated": true,
                "ani": 75.8056,
                "matched_fragments": 55,
                "total_fragments": 707,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_000765805.2",
                "gtdb_species": "s__Helicobacter_A muridarum",
                "ani": 100.0,
                "matched_fragments": 705,
                "total_fragments": 707,
                "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.98",
                "min_intra_species_ani": "99.97",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.98",
                "num_clustered_genomes": 5,
                "status": "conclusive"
            },
            {
                "accession": "GCF_000762845.2",
                "gtdb_species": "s__Helicobacter_C japonicus",
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                "matched_fragments": 53,
                "total_fragments": 707,
                "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.98",
                "min_intra_species_ani": "99.98",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_003364265.1",
                "gtdb_species": "s__Helicobacter_A aurati",
                "ani": 77.5705,
                "matched_fragments": 189,
                "total_fragments": 707,
                "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.97",
                "min_intra_species_ani": "99.97",
                "mean_intra_species_af": "0.99",
                "min_intra_species_af": "0.99",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_001999985.1",
                "gtdb_species": "s__Helicobacter_A bilis_A",
                "ani": 76.9904,
                "matched_fragments": 96,
                "total_fragments": 707,
                "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A",
                "ani_circumscription_radius": 96.3516,
                "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_000765905.2",
                "gtdb_species": "s__Helicobacter_A trogontum",
                "ani": 76.9232,
                "matched_fragments": 72,
                "total_fragments": 707,
                "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.76",
                "min_intra_species_ani": "97.01",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 5,
                "status": "-"
            },
            {
                "accession": "GCF_000762875.2",
                "gtdb_species": "s__Helicobacter_A sanguini",
                "ani": 75.8056,
                "matched_fragments": 55,
                "total_fragments": 707,
                "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A",
                "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": 5,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.302,
        "cell_length": 0.544,
        "doubling_h": 0.5,
        "growth_tmp": 37.0,
        "optimum_tmp": 36.65,
        "optimum_ph": 7.262,
        "genome_size": 2332054.0,
        "gc_content": 37.515,
        "coding_genes": 1769.479,
        "rRNA16S_genes": 1.895,
        "tRNA_genes": 37.181,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": 0.0,
        "facultative_respiration": 0.0,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 1.0,
        "mesophilic_range_tmp": 1.0,
        "thermophilic_range_tmp": 0.0,
        "psychrophilic_range_tmp": 0.0,
        "bacillus_cell_shape": 0.0,
        "coccus_cell_shape": 0.0,
        "filament_cell_shape": 0.0,
        "coccobacillus_cell_shape": 0.0,
        "vibrio_cell_shape": 0.0,
        "spiral_cell_shape": 1.0
    },
    "_genome_taxon": [
        "Helicobacter",
        "muridarum"
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}