{ "type": "genome", "identifier": "GCA_902763025.1", "organism": "uncultured Bifidobacterium sp.", "title": "uncultured Bifidobacterium sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902763025.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6148959", "wgs_master": "CACWQQ000000000.1", "refseq_category": "na", "taxid": "165187", "species_taxid": "165187", "organism_name": "uncultured Bifidobacterium sp.", "infraspecific_name": "", "isolate": "RUG10825", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/15", "asm_name": "Rumen uncultured genome RUG10825", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/763/025/GCA_902763025.1_Rumen_uncultured_genome_RUG10825", "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": "2020-02-15", "dateModified": "2020-02-15", "datePublished": "2020-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Bifidobacterium sp." ], "sample_taxid": [ "165187" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "0.513 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.46, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1808810", "Number of Sequences": "189", "Longest Sequences (bp)": "59628", "N50 (bp)": "13610", "Gap Ratio (%)": "0.024989", "GCcontent (%)": "60.0", "Number of CDSs": "1315", "Average Protein Length": "340.0", "Coding Ratio (%)": "74.1", "Number of rRNAs": "0", "Number of tRNAs": "37", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium boum", "strain": "strain=DSM 20432", "accession": "GCA_000687615.1", "taxid": 78343, "species_taxid": 78343, "relation_to_type": "type", "validated": true, "ani": 98.6904, "matched_fragments": 486, "total_fragments": 503, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium boum", "strain": "strain=LMG 10736", "accession": "GCA_000741535.1", "taxid": 78343, "species_taxid": 78343, "relation_to_type": "type", "validated": true, "ani": 98.6685, "matched_fragments": 488, "total_fragments": 503, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium boum", "strain": "strain=DSM 20432", "accession": "GCA_000771385.1", "taxid": 78343, "species_taxid": 78343, "relation_to_type": "type", "validated": true, "ani": 98.6444, "matched_fragments": 487, "total_fragments": 503, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium porcinum", "strain": "strain=DSM 17755", "accession": "GCA_000771045.1", "taxid": 212365, "species_taxid": 212365, "relation_to_type": "type", "validated": true, "ani": 86.0383, "matched_fragments": 411, "total_fragments": 503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium thermacidophilum subsp. thermacidophilum", "strain": "strain=LMG 21395", "accession": "GCA_000741455.1", "taxid": 79262, "species_taxid": 246618, "relation_to_type": "type", "validated": true, "ani": 85.7465, "matched_fragments": 413, "total_fragments": 503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium thermacidophilum subsp. thermacidophilum", "strain": "strain=DSM 15837", "accession": "GCA_000426425.1", "taxid": 79262, "species_taxid": 246618, "relation_to_type": "type", "validated": true, "ani": 85.7388, "matched_fragments": 414, "total_fragments": 503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium apri", "strain": "strain=DSM 100238", "accession": "GCA_009299485.1", "taxid": 1769423, "species_taxid": 1769423, "relation_to_type": "type", "validated": true, "ani": 85.7153, "matched_fragments": 426, "total_fragments": 503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium ruminantium", "strain": "strain=DSM 6489", "accession": "GCA_000687635.1", "taxid": 78346, "species_taxid": 78346, "relation_to_type": "type", "validated": true, "ani": 79.6406, "matched_fragments": 207, "total_fragments": 503, "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": 79.6261, "matched_fragments": 218, "total_fragments": 503, "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": 78.5898, "matched_fragments": 152, "total_fragments": 503, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.46, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000741535.1", "gtdb_species": "s__Bifidobacterium boum", "ani": 98.6685, "matched_fragments": 488, "total_fragments": 503, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "97.54", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "inconclusive" }, { "accession": "GCA_000741495.1", "gtdb_species": "s__Bifidobacterium thermophilum_A", "ani": 95.1749, "matched_fragments": 463, "total_fragments": 503, "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": "inconclusive" }, { "accession": "GCA_000771265.1", "gtdb_species": "s__Bifidobacterium thermophilum", "ani": 86.0103, "matched_fragments": 416, "total_fragments": 503, 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