{ "type": "genome", "identifier": "GCF_003315615.1", "organism": "Bifidobacterium xylocopae", "title": "Bifidobacterium xylocopae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Bologna", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003315615.1", "bioproject": "PRJNA224116", "biosample": "SAMN07723028", "wgs_master": "PDCH00000000.1", "refseq_category": "reference genome", "taxid": "2493119", "species_taxid": "2493119", "organism_name": "Bifidobacterium xylocopae", "infraspecific_name": "strain=XV2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/12", "asm_name": "ASM331561v1", "asm_submitter": "University of Bologna", "gbrs_paired_asm": "GCA_003315615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/315/615/GCF_003315615.1_ASM331561v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1848461", "genome_size_ungapped": "1848461", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "98", "contig_count": "98", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003315615.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "1578", "protein_coding_gene_count": "1479", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-12", "dateModified": "2018-07-12", "datePublished": "2018-07-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium xylocopae" ], "sample_taxid": [ "2493119" ], "sample_host_organism": [ "Xylocopa violacea" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy" ], "sample_host_location_id": [], "data_size": "0.522 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.38, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1848461", "Number of Sequences": "98", "Longest Sequences (bp)": "299711", "N50 (bp)": "107064", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.8", "Number of CDSs": "1476", "Average Protein Length": "348.9", "Coding Ratio (%)": "83.6", "Number of rRNAs": "4", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium xylocopae", "strain": "strain=XV2", "accession": "GCA_003315615.1", "taxid": 2493119, "species_taxid": 2493119, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 585, "total_fragments": 587, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium actinocoloniiforme", "strain": "strain=DSM 22766", "accession": "GCA_001263395.1", "taxid": 638619, "species_taxid": 638619, "relation_to_type": "type", "validated": true, "ani": 80.9422, "matched_fragments": 340, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium actinocoloniiforme", "strain": "strain=DSM 22766", "accession": "GCA_000741095.1", "taxid": 638619, "species_taxid": 638619, "relation_to_type": "type", "validated": true, "ani": 80.924, "matched_fragments": 328, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium actinocoloniiforme", "strain": "strain=DSM 22766", "accession": "GCA_000771585.1", "taxid": 638619, "species_taxid": 638619, "relation_to_type": "type", "validated": true, "ani": 80.7803, "matched_fragments": 327, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium apousia", "strain": "strain=W8102", "accession": "GCA_007559275.1", "taxid": 2750996, "species_taxid": 2750996, "relation_to_type": "type", "validated": true, "ani": 79.1583, "matched_fragments": 229, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium choladohabitans", "strain": "strain=B14384H11", "accession": "GCA_016102005.1", "taxid": 2750947, "species_taxid": 2750947, "relation_to_type": "type", "validated": true, "ani": 79.0808, "matched_fragments": 229, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium aemilianum", "strain": "strain=XV10", "accession": "GCA_003315635.1", "taxid": 2493120, "species_taxid": 2493120, "relation_to_type": "type", "validated": true, "ani": 79.0649, "matched_fragments": 187, "total_fragments": 587, "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": 79.0468, "matched_fragments": 218, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium asteroides", "strain": "strain=DSM 20089", "accession": "GCA_002715865.1", "taxid": 1684, "species_taxid": 1684, "relation_to_type": "suspected-type", "validated": true, "ani": 78.9883, "matched_fragments": 218, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium asteroides", "strain": "strain=DSM 20089", "accession": "GCA_000771125.1", "taxid": 1684, "species_taxid": 1684, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8599, "matched_fragments": 222, "total_fragments": 587, "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": 78.5489, "matched_fragments": 159, "total_fragments": 587, "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": 78.5045, "matched_fragments": 135, "total_fragments": 587, "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": 78.1839, "matched_fragments": 142, "total_fragments": 587, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium phasiani", "strain": "strain=6T3", "accession": 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"min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCF_001263395.1", "gtdb_species": "s__Bifidobacterium actinocoloniiforme", "ani": 80.9121, "matched_fragments": 342, "total_fragments": 587, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009683175.1", "gtdb_species": "s__Bifidobacterium asteroides_H", "ani": 79.5087, "matched_fragments": 220, "total_fragments": 587, "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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