{
    "type": "genome",
    "identifier": "GCF_003987645.1",
    "organism": "Vagococcus elongatus",
    "title": "Vagococcus elongatus",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "Centers for Disease Control and Prevention",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_003987645.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN06609012",
        "wgs_master": "NGKA00000000.1",
        "refseq_category": "reference genome",
        "taxid": "180344",
        "species_taxid": "180344",
        "organism_name": "Vagococcus elongatus",
        "infraspecific_name": "strain=CCUG 51432",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2018/12/17",
        "asm_name": "ASM398764v1",
        "asm_submitter": "Centers for Disease Control and Prevention",
        "gbrs_paired_asm": "GCA_003987645.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/987/645/GCF_003987645.1_ASM398764v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2879210",
        "genome_size_ungapped": "2879210",
        "gc_percent": "38.000000",
        "replicon_count": "0",
        "scaffold_count": "55",
        "contig_count": "55",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_003987645.1-RS_2024_05_04",
        "annotation_date": "2024-05-04",
        "total_gene_count": "2748",
        "protein_coding_gene_count": "2643",
        "non_coding_gene_count": "51",
        "pubmed_id": "na"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2018-12-17",
    "dateModified": "2018-12-17",
    "datePublished": "2018-12-17",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Vagococcus elongatus"
        ],
        "sample_taxid": [
            "180344"
        ],
        "sample_host_organism": [
            "missing"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "USA: Illinois"
        ],
        "sample_host_location_id": [],
        "data_size": "0.816 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)": "2879210",
        "Number of Sequences": "55",
        "Longest Sequences (bp)": "310847",
        "N50 (bp)": "122341",
        "Gap Ratio (%)": "0.000000",
        "GCcontent (%)": "38.1",
        "Number of CDSs": "2682",
        "Average Protein Length": "302.1",
        "Coding Ratio (%)": "84.4",
        "Number of rRNAs": "1",
        "Number of tRNAs": "45",
        "Number of CRISPRs": "2"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Vagococcus elongatus",
                "strain": "strain=CCUG 51432",
                "accession": "GCA_003987645.1",
                "taxid": 180344,
                "species_taxid": 180344,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 926,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Vagococcus acidifermentans",
                "strain": "strain=LMG 24798",
                "accession": "GCA_003987655.1",
                "taxid": 564710,
                "species_taxid": 564710,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.374,
                "matched_fragments": 70,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Vagococcus allomyrinae",
                "strain": "strain=BWB3-3",
                "accession": "GCA_017829975.1",
                "taxid": 2794353,
                "species_taxid": 2794353,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.5714,
                "matched_fragments": 58,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Enterococcus wangshanyuanii",
                "strain": "strain=CGMCC 1.15942",
                "accession": "GCA_014644255.1",
                "taxid": 2005703,
                "species_taxid": 2005703,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.4102,
                "matched_fragments": 50,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Enterococcus wangshanyuanii",
                "strain": "strain=MN05",
                "accession": "GCA_002197645.1",
                "taxid": 2005703,
                "species_taxid": 2005703,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.3226,
                "matched_fragments": 50,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Enterococcus silesiacus",
                "strain": "strain=DSM 22801",
                "accession": "GCA_001886225.1",
                "taxid": 332949,
                "species_taxid": 332949,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.1267,
                "matched_fragments": 62,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Enterococcus caccae",
                "strain": "strain=ATCC BAA-1240",
                "accession": "GCA_000407145.1",
                "taxid": 317735,
                "species_taxid": 317735,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.0866,
                "matched_fragments": 57,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Enterococcus caccae",
                "strain": "strain=ATCC BAA-1240",
                "accession": "GCA_000394055.1",
                "taxid": 317735,
                "species_taxid": 317735,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.0018,
                "matched_fragments": 58,
                "total_fragments": 931,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_003987645.1",
                "gtdb_species": "s__Vagococcus_A elongatus",
                "ani": 100.0,
                "matched_fragments": 926,
                "total_fragments": 931,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_A",
                "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_003987655.1",
                "gtdb_species": "s__Vagococcus_B acidifermentans",
                "ani": 78.2472,
                "matched_fragments": 69,
                "total_fragments": 931,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_B",
                "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_017829975.1",
                "gtdb_species": "s__Vagococcus_D sp017829975",
                "ani": 76.5714,
                "matched_fragments": 58,
                "total_fragments": 931,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Vagococcaceae;g__Vagococcus_D",
                "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_002197645.1",
                "gtdb_species": "s__Enterococcus wangshanyuanii",
                "ani": 76.3226,
                "matched_fragments": 50,
                "total_fragments": 931,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "100.00",
                "min_intra_species_ani": "100.00",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_000407145.1",
                "gtdb_species": "s__Enterococcus caccae",
                "ani": 76.0866,
                "matched_fragments": 57,
                "total_fragments": 931,
                "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "99.99",
                "min_intra_species_ani": "99.98",
                "mean_intra_species_af": "1.00",
                "min_intra_species_af": "1.00",
                "num_clustered_genomes": 4,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.302,
        "cell_length": -0.302,
        "doubling_h": null,
        "growth_tmp": 37.0,
        "optimum_tmp": 37.0,
        "optimum_ph": 6.75,
        "genome_size": 2126210.778,
        "gc_content": 34.589,
        "coding_genes": 2028.75,
        "rRNA16S_genes": 5.5,
        "tRNA_genes": 65.0,
        "gram_stain": 1.0,
        "sporulation": 0.0,
        "motility": 0.0,
        "range_salinity": null,
        "facultative_respiration": 0.285,
        "anaerobic_respiration": 0.0,
        "aerobic_respiration": 0.714,
        "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": [
        "Vagococcus",
        "elongatus"
    ],
    "quality": 3,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}