{ "type": "genome", "identifier": "GCF_000466525.1", "organism": "Bifidobacterium bifidum ATCC 29521 = JCM 1255 = DSM 20456", "title": "Bifidobacterium bifidum ATCC 29521 = JCM 1255 = DSM 20456", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Washington University Genome Sequencing Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000466525.1", "bioproject": "PRJNA224116", "biosample": "SAMN02436821", "wgs_master": "AWSW00000000.1", "refseq_category": "na", "taxid": "500634", "species_taxid": "1681", "organism_name": "Bifidobacterium bifidum ATCC 29521 = JCM 1255 = DSM 20456", "infraspecific_name": "strain=ATCC 29521", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/12", "asm_name": "ASM46652v1", "asm_submitter": "Washington University Genome Sequencing Center", "gbrs_paired_asm": "GCA_000466525.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/466/525/GCF_000466525.1_ASM46652v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2201251", "genome_size_ungapped": "2198551", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "27", "contig_count": "54", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000466525.1-RS_2024_05_15", "annotation_date": "2024-05-15", "total_gene_count": "1891", "protein_coding_gene_count": "1743", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-12", "dateModified": "2013-09-12", "datePublished": "2013-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium bifidum ATCC 29521 = JCM 1255 = DSM 20456" ], "sample_taxid": [ "500634" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.615 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)": "2201251", "Number of Sequences": "27", "Longest Sequences (bp)": "272948", "N50 (bp)": "210245", "Gap Ratio (%)": "0.122658", "GCcontent (%)": "62.7", "Number of CDSs": "1855", "Average Protein Length": "334.1", "Coding Ratio (%)": "84.5", "Number of rRNAs": "2", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium bifidum", "strain": "strain=ATCC 29521", "accession": "GCA_000466525.1", 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721, "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": 79.5979, "matched_fragments": 255, "total_fragments": 721, "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": 78.6173, "matched_fragments": 129, "total_fragments": 721, "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": 76.9269, "matched_fragments": 85, "total_fragments": 721, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001025135.1", "gtdb_species": "s__Bifidobacterium bifidum", "ani": 99.9887, "matched_fragments": 718, "total_fragments": 721, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 128, "status": "conclusive" }, { "accession": "GCF_009193355.1", "gtdb_species": "s__Bifidobacterium leontopitheci", "ani": 83.3281, "matched_fragments": 494, "total_fragments": 721, "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", 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