{
    "type": "genome",
    "identifier": "GCF_008016455.1",
    "organism": "Brachyspira aalborgi",
    "title": "Brachyspira aalborgi",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Karolinska Institutet",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_008016455.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN10696518",
        "wgs_master": "SAXU00000000.1",
        "refseq_category": "na",
        "taxid": "29522",
        "species_taxid": "29522",
        "organism_name": "Brachyspira aalborgi",
        "infraspecific_name": "strain=513A",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Scaffold",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2019/08/19",
        "asm_name": "ASM801645v1",
        "asm_submitter": "Karolinska Institutet",
        "gbrs_paired_asm": "GCA_008016455.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/016/455/GCF_008016455.1_ASM801645v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2504147",
        "genome_size_ungapped": "2503853",
        "gc_percent": "28.000000",
        "replicon_count": "0",
        "scaffold_count": "8",
        "contig_count": "8",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_008016455.1-RS_2024_03_31",
        "annotation_date": "2024-03-31",
        "total_gene_count": "2340",
        "protein_coding_gene_count": "2285",
        "non_coding_gene_count": "42",
        "pubmed_id": "1405919"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2019-08-19",
    "dateModified": "2019-08-19",
    "datePublished": "2019-08-19",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Brachyspira aalborgi"
        ],
        "sample_taxid": [
            "29522"
        ],
        "sample_host_organism": [
            "Homo sapiens"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [
            "diarrhea"
        ],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Denmark: Aalborg"
        ],
        "sample_host_location_id": [],
        "data_size": "0.667 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)": "2504147",
        "Number of Sequences": "8",
        "Longest Sequences (bp)": "2486925",
        "N50 (bp)": "2486925",
        "Gap Ratio (%)": "0.011741",
        "GCcontent (%)": "28.0",
        "Number of CDSs": "2304",
        "Average Protein Length": "320.9",
        "Coding Ratio (%)": "88.6",
        "Number of rRNAs": "3",
        "Number of tRNAs": "36",
        "Number of CRISPRs": "1"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Brachyspira aalborgi",
                "strain": "strain=513A",
                "accession": "GCA_008016455.1",
                "taxid": 29522,
                "species_taxid": 29522,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 831,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Brachyspira catarrhinii",
                "strain": "strain=Z12",
                "accession": "GCA_005518285.1",
                "taxid": 2528966,
                "species_taxid": 2528966,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.8243,
                "matched_fragments": 421,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira hyodysenteriae",
                "strain": "strain=B-78",
                "accession": "GCA_001676785.2",
                "taxid": 159,
                "species_taxid": 159,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.929,
                "matched_fragments": 279,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira hyodysenteriae",
                "strain": "strain=B78",
                "accession": "GCA_000383255.1",
                "taxid": 159,
                "species_taxid": 159,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.9043,
                "matched_fragments": 283,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira hyodysenteriae",
                "strain": "strain=B78",
                "accession": "GCA_001013005.1",
                "taxid": 159,
                "species_taxid": 159,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.873,
                "matched_fragments": 290,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira hampsonii",
                "strain": "strain=NSH-16",
                "accession": "GCA_002214805.1",
                "taxid": 1287055,
                "species_taxid": 1287055,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.6374,
                "matched_fragments": 312,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira hampsonii",
                "strain": "strain=NSH-16",
                "accession": "GCA_001746225.1",
                "taxid": 1287055,
                "species_taxid": 1287055,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.5937,
                "matched_fragments": 305,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira pilosicoli",
                "strain": "strain=P43/6/78",
                "accession": "GCA_000325665.1",
                "taxid": 52584,
                "species_taxid": 52584,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.5588,
                "matched_fragments": 274,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Brachyspira alvinipulli",
                "strain": "strain=ATCC 51933",
                "accession": "GCA_000518245.1",
                "taxid": 84379,
                "species_taxid": 84379,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.4756,
                "matched_fragments": 309,
                "total_fragments": 831,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_008016455.1",
                "gtdb_species": "s__Brachyspira aalborgi",
                "ani": 100.0,
                "matched_fragments": 831,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "95.81",
                "min_intra_species_ani": "95.36",
                "mean_intra_species_af": "0.82",
                "min_intra_species_af": "0.78",
                "num_clustered_genomes": 21,
                "status": "conclusive"
            },
            {
                "accession": "GCF_005518285.1",
                "gtdb_species": "s__Brachyspira catarrhinii",
                "ani": 84.8469,
                "matched_fragments": 420,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "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_910588665.1",
                "gtdb_species": "s__Brachyspira sp910588665",
                "ani": 76.9911,
                "matched_fragments": 268,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "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_001676785.2",
                "gtdb_species": "s__Brachyspira hyodysenteriae",
                "ani": 76.9025,
                "matched_fragments": 282,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.16",
                "min_intra_species_ani": "98.93",
                "mean_intra_species_af": "0.98",
                "min_intra_species_af": "0.95",
                "num_clustered_genomes": 58,
                "status": "-"
            },
            {
                "accession": "GCF_001746205.1",
                "gtdb_species": "s__Brachyspira hampsonii_B",
                "ani": 76.8131,
                "matched_fragments": 303,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "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_002379365.1",
                "gtdb_species": "s__Brachyspira sp002379365",
                "ani": 76.8075,
                "matched_fragments": 287,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "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_002214805.1",
                "gtdb_species": "s__Brachyspira hampsonii",
                "ani": 76.6642,
                "matched_fragments": 308,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.94",
                "min_intra_species_ani": "99.90",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 3,
                "status": "-"
            },
            {
                "accession": "GCF_000223215.1",
                "gtdb_species": "s__Brachyspira intermedia",
                "ani": 76.6218,
                "matched_fragments": 310,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "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_009755885.1",
                "gtdb_species": "s__Brachyspira sp009755885",
                "ani": 76.6077,
                "matched_fragments": 280,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "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_000325665.1",
                "gtdb_species": "s__Brachyspira pilosicoli",
                "ani": 76.5595,
                "matched_fragments": 274,
                "total_fragments": 831,
                "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "98.38",
                "min_intra_species_ani": "97.84",
                "mean_intra_species_af": "0.95",
                "min_intra_species_af": "0.91",
                "num_clustered_genomes": 19,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.456,
        "cell_length": 0.738,
        "doubling_h": 0.477,
        "growth_tmp": 37.0,
        "optimum_tmp": 37.4,
        "optimum_ph": 7.1,
        "genome_size": 3148275.979,
        "gc_content": 27.312,
        "coding_genes": 2613.666,
        "rRNA16S_genes": 1.0,
        "tRNA_genes": 33.25,
        "gram_stain": 0.0,
        "sporulation": 0.0,
        "motility": 1.0,
        "range_salinity": null,
        "facultative_respiration": 0.25,
        "anaerobic_respiration": 0.75,
        "aerobic_respiration": 0.0,
        "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": [
        "Brachyspira",
        "aalborgi"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}