{
    "type": "genome",
    "identifier": "GCF_018555385.1",
    "organism": "Bifidobacterium santillanense",
    "title": "Bifidobacterium santillanense",
    "description": "na",
    "data type": "Genome sequencing and assembly",
    "organization": "University of Parma",
    "publication": [
        {}
    ],
    "properties": {
        "assembly_accession": "GCF_018555385.1",
        "bioproject": "PRJNA224116",
        "biosample": "SAMN17736107",
        "wgs_master": "JAFEJS000000000.1",
        "refseq_category": "reference genome",
        "taxid": "2809028",
        "species_taxid": "2809028",
        "organism_name": "Bifidobacterium santillanense",
        "infraspecific_name": "strain=MA2",
        "isolate": "na",
        "version_status": "latest",
        "assembly_level": "Contig",
        "release_type": "Major",
        "genome_rep": "Full",
        "seq_rel_date": "2021/05/27",
        "asm_name": "ASM1855538v1",
        "asm_submitter": "University of Parma",
        "gbrs_paired_asm": "GCA_018555385.1",
        "paired_asm_comp": "identical",
        "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/555/385/GCF_018555385.1_ASM1855538v1",
        "excluded_from_refseq": "na",
        "relation_to_type_material": "assembly from type material",
        "asm_not_live_date": "na        ",
        "assembly_type": "haploid",
        "group": "bacteria",
        "genome_size": "2771886",
        "genome_size_ungapped": "2771886",
        "gc_percent": "66.000000",
        "replicon_count": "0",
        "scaffold_count": "25",
        "contig_count": "25",
        "annotation_provider": "NCBI RefSeq",
        "annotation_name": "GCF_018555385.1-RS_2024_03_29",
        "annotation_date": "2024-03-29",
        "total_gene_count": "2291",
        "protein_coding_gene_count": "2180",
        "non_coding_gene_count": "72",
        "pubmed_id": "33973321"
    },
    "dbXrefs": [],
    "distribution": null,
    "Download": null,
    "status": "public",
    "visibility": null,
    "dateCreated": "2021-05-27",
    "dateModified": "2021-05-27",
    "datePublished": "2021-05-27",
    "_annotation": {
        "sample_count": 1,
        "sample_organism": [
            "Bifidobacterium santillanense"
        ],
        "sample_taxid": [
            "2809028"
        ],
        "sample_host_organism": [
            "Mico argentatus"
        ],
        "sample_host_organism_id": [],
        "sample_host_disease": [],
        "sample_host_disease_id": [],
        "sample_host_location": [
            "Spain"
        ],
        "sample_host_location_id": [],
        "data_size": "0.757 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)": "2771886",
        "Number of Sequences": "25",
        "Longest Sequences (bp)": "594951",
        "N50 (bp)": "225198",
        "Gap Ratio (%)": "0.000072",
        "GCcontent (%)": "66.0",
        "Number of CDSs": "2259",
        "Average Protein Length": "351.6",
        "Coding Ratio (%)": "86.0",
        "Number of rRNAs": "4",
        "Number of tRNAs": "66",
        "Number of CRISPRs": "4"
    },
    "has_analysis": true,
    "_dfastqc": {
        "tc_result": [
            {
                "organism_name": "Bifidobacterium santillanense",
                "strain": "strain=MA2",
                "accession": "GCA_018555385.1",
                "taxid": 2809028,
                "species_taxid": 2809028,
                "relation_to_type": "type",
                "validated": true,
                "ani": 100.0,
                "matched_fragments": 909,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "conclusive"
            },
            {
                "organism_name": "Bifidobacterium rousetti",
                "strain": "strain=RST9",
                "accession": "GCA_008698235.1",
                "taxid": 2045439,
                "species_taxid": 2045439,
                "relation_to_type": "type",
                "validated": true,
                "ani": 89.1632,
                "matched_fragments": 670,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium callitrichos",
                "strain": "strain=DSM 23973",
                "accession": "GCA_000771665.1",
                "taxid": 762209,
                "species_taxid": 762209,
                "relation_to_type": "type",
                "validated": true,
                "ani": 88.7338,
                "matched_fragments": 649,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium callitrichos",
                "strain": "strain=DSM 23973",
                "accession": "GCA_000741175.1",
                "taxid": 762209,
                "species_taxid": 762209,
                "relation_to_type": "type",
                "validated": true,
                "ani": 88.6408,
                "matched_fragments": 672,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium saguinibicoloris",
                "strain": "strain=79T10",
                "accession": "GCA_019331725.1",
                "taxid": 2834433,
                "species_taxid": 2834433,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.5999,
                "matched_fragments": 589,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium parmae",
                "strain": "strain=Uis4E",
                "accession": "GCA_002860365.1",
                "taxid": 361854,
                "species_taxid": 361854,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.5525,
                "matched_fragments": 592,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium platyrrhinorum",
                "strain": "strain=SMA15",
                "accession": "GCA_010667645.1",
                "taxid": 2661628,
                "species_taxid": 2661628,
                "relation_to_type": "type",
                "validated": true,
                "ani": 87.285,
                "matched_fragments": 578,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium stellenboschense",
                "strain": "strain=DSM 23968",
                "accession": "GCA_000741785.1",
                "taxid": 762211,
                "species_taxid": 762211,
                "relation_to_type": "type",
                "validated": true,
                "ani": 86.9178,
                "matched_fragments": 583,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium amazonense",
                "strain": "strain=MA1",
                "accession": "GCA_018555435.2",
                "taxid": 2809027,
                "species_taxid": 2809027,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.7223,
                "matched_fragments": 597,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium miconisargentati",
                "strain": "strain=82T25",
                "accession": "GCA_019331675.1",
                "taxid": 2834437,
                "species_taxid": 2834437,
                "relation_to_type": "type",
                "validated": true,
                "ani": 84.6615,
                "matched_fragments": 561,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium pseudolongum subsp. pseudolongum",
                "strain": "strain=ATCC 25526",
                "accession": "GCA_022691205.1",
                "taxid": 31954,
                "species_taxid": 1694,
                "relation_to_type": "type",
                "validated": true,
                "ani": 79.7698,
                "matched_fragments": 303,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Bifidobacterium mizhiense",
                "strain": "strain=S053-2",
                "accession": "GCA_020884755.1",
                "taxid": 2879940,
                "species_taxid": 2879940,
                "relation_to_type": "type",
                "validated": true,
                "ani": 78.1002,
                "matched_fragments": 179,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            },
            {
                "organism_name": "Cellulomonas avistercoris",
                "strain": "strain=Sa3CUA2",
                "accession": "GCA_014836445.1",
                "taxid": 2762242,
                "species_taxid": 2762242,
                "relation_to_type": "type",
                "validated": true,
                "ani": 76.5101,
                "matched_fragments": 182,
                "total_fragments": 910,
                "ani_threshold": 95,
                "status": "below_threshold"
            }
        ],
        "cc_result": {
            "completeness": 100.0,
            "contamination": 0.0,
            "strain_heterogeneity": 0.0
        },
        "gtdb_result": [
            {
                "accession": "GCF_018555385.1",
                "gtdb_species": "s__Bifidobacterium sp018555385",
                "ani": 100.0,
                "matched_fragments": 909,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "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_008698235.1",
                "gtdb_species": "s__Bifidobacterium rousetti",
                "ani": 89.1632,
                "matched_fragments": 670,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.97",
                "min_intra_species_ani": "96.97",
                "mean_intra_species_af": "0.86",
                "min_intra_species_af": "0.86",
                "num_clustered_genomes": 2,
                "status": "-"
            },
            {
                "accession": "GCF_000741175.1",
                "gtdb_species": "s__Bifidobacterium callitrichos",
                "ani": 88.6408,
                "matched_fragments": 672,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "97.40",
                "min_intra_species_ani": "96.52",
                "mean_intra_species_af": "0.91",
                "min_intra_species_af": "0.88",
                "num_clustered_genomes": 6,
                "status": "-"
            },
            {
                "accession": "GCF_018555635.1",
                "gtdb_species": "s__Bifidobacterium sp018555635",
                "ani": 88.0477,
                "matched_fragments": 615,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "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_002860365.1",
                "gtdb_species": "s__Bifidobacterium parmae",
                "ani": 87.5211,
                "matched_fragments": 594,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "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_010667645.1",
                "gtdb_species": "s__Bifidobacterium platyrrhinorum",
                "ani": 87.2898,
                "matched_fragments": 577,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "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_000741785.1",
                "gtdb_species": "s__Bifidobacterium stellenboschense",
                "ani": 86.9512,
                "matched_fragments": 582,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "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_001417815.1",
                "gtdb_species": "s__Bifidobacterium aesculapii",
                "ani": 86.4667,
                "matched_fragments": 554,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "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_018555355.1",
                "gtdb_species": "s__Bifidobacterium sp018555355",
                "ani": 84.5159,
                "matched_fragments": 538,
                "total_fragments": 910,
                "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium",
                "ani_circumscription_radius": 95.0,
                "mean_intra_species_ani": "96.26",
                "min_intra_species_ani": "96.26",
                "mean_intra_species_af": "0.85",
                "min_intra_species_af": "0.85",
                "num_clustered_genomes": 2,
                "status": "-"
            }
        ]
    },
    "_bac2feature": {
        "phenotypes": null,
        "cell_diameter": -0.022,
        "cell_length": 0.328,
        "doubling_h": 0.178,
        "growth_tmp": 36.851,
        "optimum_tmp": 36.466,
        "optimum_ph": 6.377,
        "genome_size": 2304203.81,
        "gc_content": 59.795,
        "coding_genes": 1746.874,
        "rRNA16S_genes": 3.765,
        "tRNA_genes": 52.571,
        "gram_stain": 1.0,
        "sporulation": 0.0,
        "motility": 0.043,
        "range_salinity": 0.0,
        "facultative_respiration": 0.147,
        "anaerobic_respiration": 0.823,
        "aerobic_respiration": 0.029,
        "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": [
        "Bifidobacterium",
        "santillanense"
    ],
    "quality": 5,
    "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f"
}