{ "type": "genome", "identifier": "GCA_902784135.1", "organism": "uncultured Bifidobacteriaceae bacterium", "title": "uncultured Bifidobacteriaceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902784135.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6151071", "wgs_master": "CACZTM000000000.1", "refseq_category": "na", "taxid": "725926", "species_taxid": "725926", "organism_name": "uncultured Bifidobacteriaceae bacterium", "infraspecific_name": "", "isolate": "RUG12935", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/15", "asm_name": "Rumen uncultured genome RUG12935", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/784/135/GCA_902784135.1_Rumen_uncultured_genome_RUG12935", "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 Bifidobacteriaceae bacterium" ], "sample_taxid": [ "725926" ], "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": "0.524 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1856387", "Number of Sequences": "151", "Longest Sequences (bp)": "79536", "N50 (bp)": "17108", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.8", "Number of CDSs": "1276", "Average Protein Length": "368.7", "Coding Ratio (%)": "76.0", "Number of rRNAs": "0", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoscardovia suis", "strain": "strain=DSM 24744", "accession": "GCA_002797875.1", "taxid": 987063, "species_taxid": 987063, "relation_to_type": "type", "validated": true, "ani": 96.3375, "matched_fragments": 503, "total_fragments": 538, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoscardovia suis", "strain": "strain=DSM 24744", "accession": "GCA_002259715.1", "taxid": 987063, "species_taxid": 987063, "relation_to_type": "type", "validated": true, "ani": 96.3067, "matched_fragments": 504, "total_fragments": 538, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoscardovia radai", "strain": "strain=DSM 24742", "accession": "GCA_002259605.1", "taxid": 987066, "species_taxid": 987066, "relation_to_type": "type", "validated": true, "ani": 81.789, "matched_fragments": 341, "total_fragments": 538, "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": 79.3843, "matched_fragments": 164, "total_fragments": 538, "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": 79.3427, "matched_fragments": 173, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium avesanii", "strain": "strain=DSM 100685", "accession": "GCA_009299475.1", "taxid": 1798157, "species_taxid": 1798157, "relation_to_type": "type", "validated": true, "ani": 79.1754, "matched_fragments": 167, "total_fragments": 538, "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": 79.1577, "matched_fragments": 175, "total_fragments": 538, "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": 79.084, "matched_fragments": 168, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium samirii", "strain": "strain=2033B", "accession": "GCA_003952945.1", "taxid": 2306974, "species_taxid": 2306974, "relation_to_type": "type", "validated": true, "ani": 79.0814, "matched_fragments": 163, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium saimiriisciurei", "strain": "strain=SMA1", "accession": "GCA_010667655.1", "taxid": 2661627, "species_taxid": 2661627, "relation_to_type": "type", "validated": true, "ani": 79.043, "matched_fragments": 175, "total_fragments": 538, "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": 78.9754, "matched_fragments": 177, "total_fragments": 538, "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": 78.9394, "matched_fragments": 159, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium phasiani", "strain": "strain=6T3", "accession": "GCA_019331775.1", "taxid": 2834431, "species_taxid": 2834431, "relation_to_type": "type", "validated": true, "ani": 78.6466, "matched_fragments": 164, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium eulemuris", "strain": "strain=DSM 100216", "accession": "GCA_002259685.1", "taxid": 1765219, "species_taxid": 1765219, "relation_to_type": "type", "validated": true, "ani": 78.4435, "matched_fragments": 160, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium eulemuris", "strain": "strain=DSM 100216", "accession": "GCA_014898155.1", "taxid": 1765219, "species_taxid": 1765219, "relation_to_type": "type", "validated": true, "ani": 78.415, "matched_fragments": 167, "total_fragments": 538, "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": 78.2151, "matched_fragments": 137, "total_fragments": 538, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002797875.1", "gtdb_species": "s__Pseudoscardovia suis", "ani": 96.3375, "matched_fragments": 503, "total_fragments": 538, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.86", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_002259605.1", "gtdb_species": "s__Pseudoscardovia radai", "ani": 81.7887, "matched_fragments": 341, "total_fragments": 538, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia", "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_002353815.1", "gtdb_species": "s__Pseudoscardovia sp002353815", "ani": 81.3491, "matched_fragments": 289, "total_fragments": 538, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Pseudoscardovia", "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_012932365.1", "gtdb_species": "s__Bifidobacterium sp012932365", "ani": 79.3716, "matched_fragments": 178, "total_fragments": 538, "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": 79.3427, "matched_fragments": 173, "total_fragments": 538, "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_009299475.1", "gtdb_species": "s__Bifidobacterium avesanii", "ani": 79.2142, "matched_fragments": 165, "total_fragments": 538, "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_018555635.1", "gtdb_species": "s__Bifidobacterium sp018555635", "ani": 79.1871, "matched_fragments": 164, "total_fragments": 538, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, 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