{ "type": "genome", "identifier": "GCF_010667745.1", "organism": "Bifidobacterium avesanii", "title": "Bifidobacterium avesanii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Bologna", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010667745.1", "bioproject": "PRJNA224116", "biosample": "SAMN13066445", "wgs_master": "WHZY00000000.1", "refseq_category": "na", "taxid": "1798157", "species_taxid": "1798157", "organism_name": "Bifidobacterium avesanii", "infraspecific_name": "strain=TREC", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/14", "asm_name": "ASM1066774v1", "asm_submitter": "University of Bologna", "gbrs_paired_asm": "GCA_010667745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/667/745/GCF_010667745.1_ASM1066774v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2682617", "genome_size_ungapped": "2682210", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "41", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010667745.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "2122", "protein_coding_gene_count": "2035", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-14", "dateModified": "2020-02-14", "datePublished": "2020-02-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium avesanii" ], "sample_taxid": [ "1798157" ], "sample_host_organism": [ "cotton-top tamarin" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy:Verona" ], "sample_host_location_id": [], "data_size": "0.736 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)": "2682617", "Number of Sequences": "41", "Longest Sequences (bp)": "338656", "N50 (bp)": "175101", "Gap Ratio (%)": "0.015843", "GCcontent (%)": "66.3", "Number of CDSs": "2091", "Average Protein Length": "362.4", "Coding Ratio (%)": "84.7", "Number of rRNAs": "2", "Number of tRNAs": "63", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium avesanii", "strain": "strain=TREC", "accession": "GCA_010667745.1", "taxid": 1798157, "species_taxid": 1798157, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 871, "total_fragments": 872, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium avesanii", "strain": "strain=DSM 100685", "accession": "GCA_009299475.1", "taxid": 1798157, "species_taxid": 1798157, "relation_to_type": "type", "validated": true, "ani": 99.9813, "matched_fragments": 867, "total_fragments": 872, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium vespertilionis", "strain": "strain=RST16", "accession": "GCA_008698145.1", "taxid": 2562524, "species_taxid": 2562524, "relation_to_type": "type", "validated": true, "ani": 86.948, "matched_fragments": 625, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium santillanense", "strain": "strain=MA2", "accession": "GCA_018555385.1", "taxid": 2809028, "species_taxid": 2809028, "relation_to_type": "type", "validated": true, "ani": 83.9026, "matched_fragments": 486, "total_fragments": 872, "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": 83.7647, "matched_fragments": 477, "total_fragments": 872, "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": 83.6206, "matched_fragments": 459, "total_fragments": 872, "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": 83.4779, "matched_fragments": 463, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium rousetti", "strain": "strain=RST9", "accession": "GCA_008698235.1", "taxid": 2045439, "species_taxid": 2045439, "relation_to_type": "type", "validated": true, "ani": 83.3135, "matched_fragments": 474, "total_fragments": 872, "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": 83.2626, "matched_fragments": 476, "total_fragments": 872, "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": 83.2335, "matched_fragments": 482, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium callitrichidarum", "strain": "strain=TRI 5", "accession": "GCA_003129905.1", "taxid": 2052941, "species_taxid": 2052941, "relation_to_type": "type", "validated": true, "ani": 82.9404, "matched_fragments": 471, "total_fragments": 872, "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": 82.9238, "matched_fragments": 448, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium scardovii", "strain": "strain=DSM 13734", "accession": "GCA_000770985.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 82.7743, "matched_fragments": 464, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium scardovii", "strain": "strain=DSM 13734", "accession": "GCA_001005065.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 82.6858, "matched_fragments": 476, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium catulorum", "strain": "strain=MRM 8.19", "accession": "GCA_003129925.1", "taxid": 1630173, "species_taxid": 1630173, "relation_to_type": "type", "validated": true, "ani": 81.6243, "matched_fragments": 357, "total_fragments": 872, "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": 79.9591, "matched_fragments": 304, "total_fragments": 872, "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": 78.5178, "matched_fragments": 184, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas palmilytica", "strain": "strain=EW123", "accession": "GCA_021590045.1", "taxid": 2608402, "species_taxid": 2608402, "relation_to_type": "type", "validated": true, "ani": 76.7443, "matched_fragments": 167, "total_fragments": 872, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009299475.1", "gtdb_species": "s__Bifidobacterium avesanii", "ani": 99.9813, "matched_fragments": 867, "total_fragments": 872, "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": "conclusive" }, { "accession": "GCF_012932365.1", "gtdb_species": "s__Bifidobacterium sp012932365", "ani": 87.1942, "matched_fragments": 608, "total_fragments": 872, "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_008698145.1", "gtdb_species": "s__Bifidobacterium vespertilionis", "ani": 86.9594, "matched_fragments": 624, "total_fragments": 872, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.94", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018555385.1", "gtdb_species": "s__Bifidobacterium sp018555385", "ani": 83.8876, "matched_fragments": 488, "total_fragments": 872, "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": 83.7597, "matched_fragments": 477, "total_fragments": 872, "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": 83.6059, "matched_fragments": 460, "total_fragments": 872, "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": 83.4586, "matched_fragments": 464, "total_fragments": 872, "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_008698235.1", "gtdb_species": "s__Bifidobacterium rousetti", "ani": 83.3422, "matched_fragments": 472, "total_fragments": 872, "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_003129905.1", "gtdb_species": "s__Bifidobacterium callitrichidarum", "ani": 82.9365, "matched_fragments": 471, "total_fragments": 872, "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_000741175.1", "gtdb_species": "s__Bifidobacterium callitrichos", "ani": 82.8681, "matched_fragments": 450, "total_fragments": 872, "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_001042635.1", "gtdb_species": "s__Bifidobacterium scardovii", "ani": 82.5945, "matched_fragments": 485, "total_fragments": 872, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.51", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003129925.1", "gtdb_species": "s__Galliscardovia catulorum", "ani": 81.6458, "matched_fragments": 357, "total_fragments": 872, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "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_002298605.1", "gtdb_species": "s__Bifidobacterium sp002298605", "ani": 81.4013, "matched_fragments": 349, "total_fragments": 872, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "99.49", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "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", "avesanii" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }