{ "type": "genome", "identifier": "GCF_000741575.1", "organism": "Bifidobacterium cuniculi", "title": "Bifidobacterium cuniculi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Parma", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000741575.1", "bioproject": "PRJNA224116", "biosample": "SAMN02673433", "wgs_master": "JGYV00000000.1", "refseq_category": "reference genome", "taxid": "1688", "species_taxid": "1688", "organism_name": "Bifidobacterium cuniculi", "infraspecific_name": "strain=LMG 10738", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/08/18", "asm_name": "Bifcun", "asm_submitter": "University of Parma", "gbrs_paired_asm": "GCA_000741575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/741/575/GCF_000741575.1_Bifcun", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2531592", "genome_size_ungapped": "2531592", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "41", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000741575.1-RS_2024_03_27", "annotation_date": "2024-03-27", "total_gene_count": "2317", "protein_coding_gene_count": "2202", "non_coding_gene_count": "77", "pubmed_id": "25085493;25107967" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-08-18", "dateModified": "2014-08-18", "datePublished": "2014-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium cuniculi" ], "sample_taxid": [ "1688" ], "sample_host_organism": [ "rabbit" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.701 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)": "2531592", "Number of Sequences": "41", "Longest Sequences (bp)": "779775", "N50 (bp)": "108872", "Gap Ratio (%)": "0.000040", "GCcontent (%)": "64.9", "Number of CDSs": "2251", "Average Protein Length": "326.7", "Coding Ratio (%)": "87.2", "Number of rRNAs": "1", "Number of tRNAs": "64", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium cuniculi", "strain": "strain=LMG 10738", "accession": "GCA_000741575.1", "taxid": 1688, "species_taxid": 1688, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 822, "total_fragments": 824, "ani_threshold": 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"GCA_014836445.1", "taxid": 2762242, "species_taxid": 2762242, "relation_to_type": "type", "validated": true, "ani": 76.0967, "matched_fragments": 115, "total_fragments": 824, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000741575.1", "gtdb_species": "s__Bifidobacterium cuniculi", "ani": 100.0, "matched_fragments": 822, "total_fragments": 824, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002286915.1", "gtdb_species": "s__Bifidobacterium italicum", "ani": 82.4191, "matched_fragments": 429, "total_fragments": 824, "gtdb_taxonomy": 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