{
    "type": "genome",
    "identifier": "GCF_022936085.1",
    "organism": "Orientia tsutsugamushi str. Karp",
    "title": "Orientia tsutsugamushi str. Karp",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "University of Texas Medical Branch",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_022936085.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN26527628",
        "wgs_master": "na",
        "refseq_category": "na",
        "taxid": "1359185",
        "species_taxid": "784",
        "organism_name": "Orientia tsutsugamushi str. Karp",
        "infraspecific_name": "strain=Karp",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Complete Genome",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2022/04/12",
        "asm_name": "ASM2293608v1",
        "asm_submitter": "University of Texas Medical Branch",
        "gbrs_paired_asm": "GCA_022936085.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/022/936/085/GCF_022936085.1_ASM2293608v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2468706",
        "genome_size_ungapped": "2468706",
        "gc_percent": "31.000000",
        "replicon_count": "1",
        "scaffold_count": "1",
        "contig_count": "1",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_022936085.1-RS_2024_04_28",
        "annotation_date": "2024-04-28",
        "total_gene_count": "2692",
        "protein_coding_gene_count": "1967",
        "non_coding_gene_count": "40",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2022-04-12",
    "dateModified": "2022-04-12",
    "datePublished": "2022-04-12",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Orientia tsutsugamushi str. Karp"
        ],
        "sample_taxid": [
            "1359185"
        ],
        "sample_host_organism": [
            "Homo sapiens"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [
            "Scrub typhus"
        ],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "not collected"
        ],
        "sample_host_location_id": [],
        "data_size": "0.667 MB",
        "sample_ph_range": {
            "min": null,
            "max": null
        },
        "sample_temperature_range": {
            "min": null,
            "max": null
        },
        "completeness": 95.45,
        "contamination": 0.0,
        "strain_heterogeneity": 0.0,
        "genome_count": 1
    },
    "data_type": "G",
    "data_source": "RefSeq",
    "_dfast": {
        "Total Sequence Length (bp)": "2468706",
        "Number of Sequences": "1",
        "Longest Sequences (bp)": "2468706",
        "N50 (bp)": "2468706",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "30.8",
        "Number of CDSs": "2790",
        "Average Protein Length": "226.0",
        "Coding Ratio (%)": "76.6",
        "Number of rRNAs": "2",
        "Number of tRNAs": "34",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Orientia tsutsugamushi",
                "strain": "strain=Karp",
                "accession": "GCA_022936085.1",
                "taxid": 784,
                "species_taxid": 784,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 815,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Orientia tsutsugamushi",
                "strain": "",
                "accession": "GCA_900327275.1",
                "taxid": 784,
                "species_taxid": 784,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 99.9663,
                "matched_fragments": 814,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Orientia tsutsugamushi",
                "strain": "strain=Karp",
                "accession": "GCA_001654785.2",
                "taxid": 784,
                "species_taxid": 784,
                "relation_to_type": "suspected-type",
                "validated": true,
                "ani": 99.8664,
                "matched_fragments": 602,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Orientia chuto",
                "strain": "strain=Dubai",
                "accession": "GCA_000964595.1",
                "taxid": 911112,
                "species_taxid": 911112,
                "relation_to_type": "type",
                "validated": true,
                "ani": 81.3781,
                "matched_fragments": 258,
                "total_fragments": 822,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 95.45,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_900327275.1",
                "gtdb_species": "s__Orientia tsutsugamushi",
                "ani": 99.9663,
                "matched_fragments": 814,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Orientia",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.28",
                "min_intra_species_ani": "95.31",
                "mean_intra_species_af": "0.83",
                "min_intra_species_af": "0.66",
                "num_clustered_genomes": 17,
                "status": "conclusive"
            },
            {
                "accession": "GCF_000964595.1",
                "gtdb_species": "s__Orientia chuto",
                "ani": 81.3665,
                "matched_fragments": 258,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Orientia",
                "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_000309075.1",
                "gtdb_species": "s__Occidentia massiliensis",
                "ani": 77.0369,
                "matched_fragments": 67,
                "total_fragments": 822,
                "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Rickettsiaceae;g__Occidentia",
                "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": null,
        "cell_length": null,
        "doubling_h": null,
        "growth_tmp": null,
        "optimum_tmp": null,
        "optimum_ph": null,
        "genome_size": 2052402.708,
        "gc_content": 30.54,
        "coding_genes": 1638.091,
        "rRNA16S_genes": 1.0,
        "tRNA_genes": 34.222,
        "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": 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": [
        "Orientia",
        "tsutsugamushi",
        "str.",
        "Karp"
    ],
    "quality": 4,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}