{ "type": "genome", "identifier": "GCF_000771505.1", "organism": "Bifidobacterium pullorum subsp. gallinarum DSM 20670", "title": "Bifidobacterium pullorum subsp. gallinarum DSM 20670", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Key Laboratory of Dairy BiotecInner Mongolia Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000771505.1", "bioproject": "PRJNA224116", "biosample": "SAMN02442031", "wgs_master": "JDUN00000000.1", "refseq_category": "na", "taxid": "1437602", "species_taxid": "78448", "organism_name": "Bifidobacterium pullorum subsp. gallinarum DSM 20670", "infraspecific_name": "strain=DSM 20670", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/11/04", "asm_name": "DSM-20670", "asm_submitter": "Key Laboratory of Dairy BiotecInner Mongolia Agricultural University", "gbrs_paired_asm": "GCA_000771505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/771/505/GCF_000771505.1_DSM-20670", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2128566", "genome_size_ungapped": "2128566", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "103", "contig_count": "103", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000771505.1-RS_2024_03_30", "annotation_date": "2024-03-30", "total_gene_count": "1842", "protein_coding_gene_count": "1723", "non_coding_gene_count": "61", "pubmed_id": "25658111" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-11-04", "dateModified": "2014-11-04", "datePublished": "2014-11-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium pullorum subsp. gallinarum DSM 20670" ], "sample_taxid": [ "1437602" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.592 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)": "2128566", "Number of Sequences": "103", "Longest Sequences (bp)": "284377", "N50 (bp)": "144807", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.2", "Number of CDSs": "1691", "Average Protein Length": "361.1", "Coding Ratio (%)": "86.1", "Number of rRNAs": "0", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium pullorum subsp. gallinarum", "strain": "strain=DSM 20670", "accession": "GCA_000771505.1", "taxid": 78344, "species_taxid": 78448, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 673, "total_fragments": 675, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium pullorum subsp. gallinarum", "strain": "strain=LMG 11586", "accession": "GCA_000741215.1", "taxid": 78344, "species_taxid": 78448, "relation_to_type": "type", "validated": true, "ani": 99.997, "matched_fragments": 674, "total_fragments": 675, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium pullorum subsp. saeculare", "strain": "strain=LMG 14934", "accession": "GCA_000741375.1", "taxid": 78257, "species_taxid": 78448, "relation_to_type": "type", "validated": true, "ani": 97.1223, "matched_fragments": 590, "total_fragments": 675, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium pullorum subsp. saeculare", "strain": "strain=DSM 6531", "accession": "GCA_000770965.1", "taxid": 78257, "species_taxid": 78448, "relation_to_type": "type", "validated": true, "ani": 97.096, "matched_fragments": 577, "total_fragments": 675, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium phasiani", "strain": "strain=6T3", "accession": "GCA_019331775.1", "taxid": 2834431, "species_taxid": 2834431, "relation_to_type": "type", "validated": true, "ani": 85.057, "matched_fragments": 514, "total_fragments": 675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium santillanense", "strain": "strain=MA2", "accession": "GCA_018555385.1", "taxid": 2809028, "species_taxid": 2809028, "relation_to_type": "type", "validated": true, "ani": 82.0949, "matched_fragments": 384, "total_fragments": 675, "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": 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true, "ani": 76.4758, "matched_fragments": 91, "total_fragments": 675, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occultella glacieicola", "strain": "strain=T3246-1", "accession": "GCA_004353825.1", "taxid": 2518684, "species_taxid": 2518684, "relation_to_type": "type", "validated": true, "ani": 76.0536, "matched_fragments": 91, "total_fragments": 675, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000741215.1", "gtdb_species": "s__Bifidobacterium pullorum_B", "ani": 99.997, "matched_fragments": 674, "total_fragments": 675, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.16", "min_intra_species_ani": "95.67", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", 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"num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001042635.1", "gtdb_species": "s__Bifidobacterium scardovii", "ani": 82.2304, "matched_fragments": 427, "total_fragments": 675, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.51", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003952945.1", "gtdb_species": "s__Bifidobacterium samirii", "ani": 82.1744, "matched_fragments": 410, "total_fragments": 675, "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": 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"cell_diameter": 0.301, "cell_length": 0.328, "doubling_h": 0.178, "growth_tmp": 37.0, "optimum_tmp": 36.466, "optimum_ph": 6.377, "genome_size": 2123679.0, "gc_content": 59.795, "coding_genes": 1746.874, "rRNA16S_genes": 3.765, "tRNA_genes": 52.571, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.043, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Bifidobacterium", "pullorum", "subsp.", "gallinarum", "DSM", "20670" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }