{ "type": "genome", "identifier": "GCF_000737845.1", "organism": "Bifidobacterium bombi DSM 19703", "title": "Bifidobacterium bombi DSM 19703", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Parma", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000737845.1", "bioproject": "PRJNA224116", "biosample": "SAMN02952076", "wgs_master": "ATLK00000000.1", "refseq_category": "na", "taxid": "1341695", "species_taxid": "471511", "organism_name": "Bifidobacterium bombi DSM 19703", "infraspecific_name": "strain=DSM 19703", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/08/05", "asm_name": "BBOMBassembly", "asm_submitter": "University of Parma", "gbrs_paired_asm": "GCA_000737845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/737/845/GCF_000737845.1_BBOMBassembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1895239", "genome_size_ungapped": "1895239", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-07", "total_gene_count": "1486", "protein_coding_gene_count": "1397", "non_coding_gene_count": "54", "pubmed_id": "25085493" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-08-05", "dateModified": "2014-08-05", "datePublished": "2014-08-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium bombi DSM 19703" ], "sample_taxid": [ "1341695" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.540 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": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1895239", "Number of Sequences": "4", "Longest Sequences (bp)": "1617820", "N50 (bp)": "1617820", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.1", "Number of CDSs": "1512", "Average Protein Length": "344.1", "Coding Ratio (%)": "82.4", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium bombi", "strain": "strain=DSM 19703", "accession": "GCA_000737845.1", "taxid": 471511, "species_taxid": 471511, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 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"below_threshold" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=LMG 11597", "accession": "GCA_000741775.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 77.4234, "matched_fragments": 110, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium commune", "strain": "strain=DSM 28792", "accession": "GCA_014191315.1", "taxid": 1505727, "species_taxid": 1505727, "relation_to_type": "type", "validated": true, "ani": 77.4102, "matched_fragments": 87, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium catulorum", "strain": "strain=MRM 8.19", "accession": "GCA_003129925.1", "taxid": 1630173, "species_taxid": 1630173, "relation_to_type": "type", "validated": true, "ani": 77.3677, "matched_fragments": 88, "total_fragments": 630, "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": 77.3566, "matched_fragments": 87, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium merycicum", "strain": "strain=DSM 6492", "accession": "GCA_900129045.1", "taxid": 78345, "species_taxid": 78345, "relation_to_type": "type", "validated": true, "ani": 77.3379, "matched_fragments": 92, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium adolescentis", "strain": "strain=NCTC11814", "accession": "GCA_900445615.1", "taxid": 1680, "species_taxid": 1680, "relation_to_type": "type", "validated": true, "ani": 77.3296, "matched_fragments": 84, "total_fragments": 630, "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": 77.3123, "matched_fragments": 96, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=DSM 20096", "accession": "GCA_000426405.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 77.2923, "matched_fragments": 113, "total_fragments": 630, "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": 77.2613, "matched_fragments": 83, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium leontopitheci", "strain": "strain=LMG 31471", "accession": "GCA_009193355.1", "taxid": 2650774, "species_taxid": 2650774, "relation_to_type": "type", "validated": true, "ani": 77.2527, "matched_fragments": 94, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium thermacidophilum subsp. thermacidophilum", "strain": "strain=DSM 15837", "accession": "GCA_000771005.1", "taxid": 79262, "species_taxid": 246618, "relation_to_type": "type", "validated": true, "ani": 77.2299, "matched_fragments": 82, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium scardovii", "strain": "strain=JCM 12489", "accession": "GCA_001042635.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 77.2272, "matched_fragments": 108, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=DSM 20096", "accession": "GCA_000771185.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 77.2268, "matched_fragments": 114, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium scardovii", "strain": "strain=DSM 13734", "accession": "GCA_000770985.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 77.1872, "matched_fragments": 101, "total_fragments": 630, "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": 77.1772, "matched_fragments": 84, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium scardovii", "strain": "strain=DSM 13734", "accession": "GCA_001005065.1", "taxid": 158787, "species_taxid": 158787, "relation_to_type": "type", "validated": true, "ani": 77.1674, "matched_fragments": 103, "total_fragments": 630, "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": 77.0854, "matched_fragments": 81, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium aesculapii", "strain": "strain=DSM 26737", "accession": "GCA_001417815.1", "taxid": 1329411, "species_taxid": 1329411, "relation_to_type": "type", "validated": true, "ani": 77.0282, "matched_fragments": 90, "total_fragments": 630, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000737845.1", "gtdb_species": 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stellenboschense", "ani": 77.5358, "matched_fragments": 88, "total_fragments": 630, "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_002259745.1", "gtdb_species": "s__Bifidobacterium myosotis", "ani": 77.496, "matched_fragments": 90, "total_fragments": 630, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.86", "min_intra_species_ani": "96.74", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009371885.1", "gtdb_species": "s__Bifidobacterium tibiigranuli", 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