{ "type": "genome", "identifier": "GCF_002259645.1", "organism": "Bifidobacterium tissieri", "title": "Bifidobacterium tissieri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Parma", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002259645.1", "bioproject": "PRJNA224116", "biosample": "SAMN06341151", "wgs_master": "MWWV00000000.1", "refseq_category": "reference genome", "taxid": "1630162", "species_taxid": "1630162", "organism_name": "Bifidobacterium tissieri", "infraspecific_name": "strain=DSM 100201", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/08/18", "asm_name": "ASM225964v1", "asm_submitter": "University of Parma", "gbrs_paired_asm": "GCA_002259645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/259/645/GCF_002259645.1_ASM225964v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2873483", "genome_size_ungapped": "2873483", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "38", "contig_count": "38", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002259645.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2326", "protein_coding_gene_count": "2214", "non_coding_gene_count": "79", "pubmed_id": "28764658" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-08-18", "dateModified": "2017-08-18", "datePublished": "2017-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium tissieri" ], "sample_taxid": [ "1630162" ], "sample_host_organism": [ "common marmosets" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy" ], "sample_host_location_id": [], "data_size": "0.803 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)": "2873483", "Number of Sequences": "38", "Longest Sequences (bp)": "405492", "N50 (bp)": "210583", "Gap Ratio (%)": "0.000592", "GCcontent (%)": "61.1", "Number of CDSs": "2235", "Average Protein Length": "359.5", "Coding Ratio (%)": "83.9", "Number of rRNAs": "2", "Number of tRNAs": "60", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium tissieri", "strain": "strain=DSM 100201", "accession": "GCA_002259645.1", "taxid": 1630162, "species_taxid": 1630162, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 938, 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"status": "below_threshold" }, { "organism_name": "Bifidobacterium primatium", "strain": "strain=TRE 1", "accession": "GCA_002802875.1", "taxid": 2045438, "species_taxid": 2045438, "relation_to_type": "type", "validated": true, "ani": 83.2846, "matched_fragments": 533, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium pluvialisilvae", "strain": "strain=82T24", "accession": "GCA_019331695.1", "taxid": 2834436, "species_taxid": 2834436, "relation_to_type": "type", "validated": true, "ani": 82.9409, "matched_fragments": 535, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium simiarum", "strain": "strain=TRI 7", "accession": "GCA_002802905.1", "taxid": 2045441, "species_taxid": 2045441, "relation_to_type": "type", "validated": true, "ani": 82.618, "matched_fragments": 504, "total_fragments": 940, "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": 80.7076, "matched_fragments": 359, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium ramosum", "strain": "strain=TREM", "accession": "GCA_010667665.1", "taxid": 1798158, "species_taxid": 1798158, "relation_to_type": "type", "validated": true, "ani": 80.6717, "matched_fragments": 362, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium aerophilum", "strain": "strain=TRE17", "accession": "GCA_010667685.1", "taxid": 1798155, "species_taxid": 1798155, "relation_to_type": "type", "validated": true, "ani": 80.3617, "matched_fragments": 366, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium epidermidis", "strain": "strain=Marseille-Q2903", "accession": "GCA_015209585.1", "taxid": 2781983, "species_taxid": 2781983, "relation_to_type": "type", "validated": true, "ani": 76.2656, "matched_fragments": 71, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Promicromonospora umidemergens", "strain": "strain=DSM 22081", "accession": "GCA_024171995.1", "taxid": 629679, "species_taxid": 629679, "relation_to_type": "type", "validated": true, "ani": 76.2509, "matched_fragments": 75, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces apocyni", "strain": "strain=TRM 66233", "accession": "GCA_009739465.1", "taxid": 2654677, "species_taxid": 2654677, "relation_to_type": "type", "validated": true, "ani": 75.6817, "matched_fragments": 60, "total_fragments": 940, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, 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{ "accession": "GCF_003952005.1", "gtdb_species": "s__Galliscardovia callimiconis", "ani": 87.4565, "matched_fragments": 727, "total_fragments": 940, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "98.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010667655.1", "gtdb_species": "s__Galliscardovia saimiriisciurei", "ani": 83.3282, "matched_fragments": 537, "total_fragments": 940, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { 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"gtdb_species": "s__Galliscardovia simiarum", "ani": 82.618, "matched_fragments": 504, "total_fragments": 940, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009299505.1", "gtdb_species": "s__Bifidobacterium ramosum", "ani": 80.5435, "matched_fragments": 360, "total_fragments": 940, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010667685.1", "gtdb_species": "s__Bifidobacterium aerophilum", "ani": 80.3615, "matched_fragments": 366, "total_fragments": 940, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.022, "cell_length": 0.328, "doubling_h": 0.178, "growth_tmp": 37.0, "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", "tissieri" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }