{ "type": "genome", "identifier": "GCA_947253155.1", "organism": "uncultured Bifidobacteriaceae bacterium", "title": "uncultured Bifidobacteriaceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "EMG", "publication": [ {} ], "properties": { "assembly_accession": "GCA_947253155.1", "bioproject": "PRJEB56771", "biosample": "SAMEA111539279", "wgs_master": "CAMXYK000000000.1", "refseq_category": "na", "taxid": "725926", "species_taxid": "725926", "organism_name": "uncultured Bifidobacteriaceae bacterium", "infraspecific_name": "", "isolate": "SRR17635716_bin.2_metaWRAP_v1.3_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/04", "asm_name": "SRR17635716_bin.2_metaWRAP_v1.3_MAG", "submitter": "EMG", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/947/253/155/GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-11-04", "dateModified": "2022-11-04", "datePublished": "2022-11-04", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Bifidobacteriaceae bacterium" ], "sample_taxid": [ "725926" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.328 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.29, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1151721", "Number of Sequences": "31", "Longest Sequences (bp)": "128076", "N50 (bp)": "65866", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.1", "Number of CDSs": "853", "Average Protein Length": "388.3", "Coding Ratio (%)": "86.3", "Number of rRNAs": "0", "Number of tRNAs": "35", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gardnerella swidsinskii", "strain": "strain=GS 9838-1", "accession": "GCA_003397705.1", "taxid": 2792979, "species_taxid": 2792979, "relation_to_type": "type", "validated": true, "ani": 86.073, "matched_fragments": 306, "total_fragments": 372, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella leopoldii", "strain": "strain=UGent 06.41", "accession": "GCA_003293675.1", "taxid": 2792978, "species_taxid": 2792978, "relation_to_type": "type", "validated": true, "ani": 85.8965, "matched_fragments": 303, "total_fragments": 372, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella vaginalis", "strain": "strain=DSM 4944", "accession": "GCA_900105405.1", "taxid": 2702, "species_taxid": 2702, "relation_to_type": "suspected-type", "validated": true, "ani": 82.5534, "matched_fragments": 220, "total_fragments": 372, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella piotii", "strain": "strain=UGent 18.01", "accession": "GCA_003397585.1", "taxid": 2792977, "species_taxid": 2792977, "relation_to_type": "type", "validated": true, "ani": 82.3236, "matched_fragments": 228, "total_fragments": 372, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gardnerella vaginalis", "strain": "strain=ATCC 14018", "accession": "GCA_000178355.1", "taxid": 2702, "species_taxid": 2702, "relation_to_type": "suspected-type", "validated": true, "ani": 82.157, "matched_fragments": 193, "total_fragments": 372, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.29, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_003585735.1", "gtdb_species": "s__Bifidobacterium sp003585735", "ani": 94.5787, "matched_fragments": 353, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "99.73", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000263635.1", "gtdb_species": "s__Bifidobacterium vaginale_C", "ani": 88.6793, "matched_fragments": 323, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.53", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000263595.1", "gtdb_species": "s__Bifidobacterium vaginale_E", "ani": 87.9564, "matched_fragments": 324, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.68", "min_intra_species_ani": "95.61", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_003585845.1", "gtdb_species": "s__Bifidobacterium sp003585845", "ani": 86.2191, "matched_fragments": 319, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.706, "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_001546485.1", "gtdb_species": "s__Bifidobacterium vaginale_D", "ani": 86.132, "matched_fragments": 298, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.82", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003408845.1", "gtdb_species": "s__Bifidobacterium vaginale_H", "ani": 86.1249, "matched_fragments": 292, "total_fragments": 372, "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_003397705.1", "gtdb_species": "s__Bifidobacterium swidsinskii", "ani": 86.029, "matched_fragments": 308, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.6629, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_003293675.1", "gtdb_species": "s__Bifidobacterium leopoldii", "ani": 85.8666, "matched_fragments": 304, "total_fragments": 372, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.706, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_002896555.1", "gtdb_species": "s__Bifidobacterium vaginale_F", "ani": 83.8543, "matched_fragments": 232, "total_fragments": 372, "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": -0.07, "cell_length": 0.302, "doubling_h": 0.178, "growth_tmp": 36.847, "optimum_tmp": 36.523, "optimum_ph": 6.635, "genome_size": 2234587.544, "gc_content": 57.64, "coding_genes": 1696.67, "rRNA16S_genes": 3.486, "tRNA_genes": 51.485, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.034, "range_salinity": 0.2, "facultative_respiration": 0.162, "anaerobic_respiration": 0.767, "aerobic_respiration": 0.069, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.925, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.074, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Actinomycetota", "c__Actinomycetes", "o__Actinomycetales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__Bifidobacterium sp947253155" ], "_genome_taxon": [ "uncultured", "Bifidobacteriaceae", "bacterium", "d__Bacteria", "p__Actinomycetota", "c__Actinomycetes", "o__Actinomycetales", "f__Bifidobacteriaceae", "g__Bifidobacterium", "s__Bifidobacterium sp947253155", "Bacteria", "Actinomycetota", "Actinomycetes", "Actinomycetales", "Bifidobacteriaceae", "Bifidobacterium", "Bifidobacterium", "sp947253155" ], "_meo": [ { "id": "MEO_0000523", "label": "vagina" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }