{ "type": "genome", "identifier": "GCF_000426405.1", "organism": "Bifidobacterium subtile DSM 20096", "title": "Bifidobacterium subtile DSM 20096", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000426405.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440843", "wgs_master": "AUFH00000000.1", "refseq_category": "na", "taxid": "1121110", "species_taxid": "77635", "organism_name": "Bifidobacterium subtile DSM 20096", "infraspecific_name": "strain=DSM 20096", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/10", "asm_name": "ASM42640v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000426405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/426/405/GCF_000426405.1_ASM42640v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2765266", "genome_size_ungapped": "2765266", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "32", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000426405.1-RS_2024_05_15", "annotation_date": "2024-05-15", "total_gene_count": "2315", "protein_coding_gene_count": "2194", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-10", "dateModified": "2013-07-10", "datePublished": "2013-07-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Bifidobacterium subtile DSM 20096" ], "sample_taxid": [ "1121110" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.778 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)": "2765266", "Number of Sequences": "32", "Longest Sequences (bp)": "503927", "N50 (bp)": "237138", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.9", "Number of CDSs": "2263", "Average Protein Length": "338.0", "Coding Ratio (%)": "83.0", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bifidobacterium subtile", "strain": "strain=DSM 20096", "accession": "GCA_000426405.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 900, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=LMG 11597", "accession": "GCA_000741775.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 99.9867, "matched_fragments": 897, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=DSM 20096", "accession": "GCA_000771185.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 99.9764, "matched_fragments": 878, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bifidobacterium tibiigranuli", "strain": "strain=TMW 2.2057", "accession": "GCA_009371885.1", "taxid": 2172043, "species_taxid": 2172043, "relation_to_type": "type", "validated": true, "ani": 89.4309, "matched_fragments": 682, "total_fragments": 902, "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": 79.8675, "matched_fragments": 337, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium miconis", "strain": "strain=82T10", "accession": "GCA_019331735.1", "taxid": 2834435, "species_taxid": 2834435, "relation_to_type": "type", "validated": true, "ani": 79.7408, "matched_fragments": 319, "total_fragments": 902, "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": "type", "validated": true, "ani": 79.5745, "matched_fragments": 322, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium mongoliense", "strain": "strain=DSM 21395", "accession": "GCA_000771525.1", "taxid": 518643, "species_taxid": 518643, "relation_to_type": "type", "validated": true, "ani": 79.5724, "matched_fragments": 288, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium ramosum", "strain": "strain=TREM", "accession": "GCA_010667665.1", "taxid": 1798158, "species_taxid": 1798158, "relation_to_type": "type", "validated": true, "ani": 79.4331, "matched_fragments": 312, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "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": 79.4331, "matched_fragments": 309, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium miconisargentati", "strain": "strain=82T25", "accession": "GCA_019331675.1", "taxid": 2834437, "species_taxid": 2834437, "relation_to_type": "type", "validated": true, "ani": 79.0992, "matched_fragments": 312, "total_fragments": 902, "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": 78.6163, "matched_fragments": 224, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas fulva", "strain": "strain=DKR-3", "accession": "GCA_018531375.1", "taxid": 2835530, "species_taxid": 2835530, "relation_to_type": "type", "validated": true, "ani": 76.2282, "matched_fragments": 69, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces harenosi", "strain": "strain=PRKS01-65", "accession": "GCA_011008945.1", "taxid": 2697029, "species_taxid": 2697029, "relation_to_type": "type", "validated": true, "ani": 75.6329, "matched_fragments": 75, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000741775.1", "gtdb_species": "s__Bifidobacterium subtile", "ani": 99.9867, "matched_fragments": 897, "total_fragments": 902, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_009371885.1", "gtdb_species": "s__Bifidobacterium tibiigranuli", "ani": 89.4127, "matched_fragments": 683, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001042635.1", "gtdb_species": "s__Bifidobacterium scardovii", "ani": 79.8821, "matched_fragments": 349, "total_fragments": 902, "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_000741285.1", "gtdb_species": "s__Bifidobacterium mongoliense", "ani": 79.7438, "matched_fragments": 289, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "98.93", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000771405.1", "gtdb_species": "s__Bifidobacterium pullorum", "ani": 79.7224, "matched_fragments": 289, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_012932365.1", "gtdb_species": "s__Bifidobacterium sp012932365", "ani": 79.526, "matched_fragments": 297, "total_fragments": 902, "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_010667645.1", "gtdb_species": "s__Bifidobacterium platyrrhinorum", "ani": 79.4664, "matched_fragments": 324, "total_fragments": 902, "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_003952945.1", "gtdb_species": "s__Bifidobacterium samirii", "ani": 79.4619, "matched_fragments": 301, "total_fragments": 902, "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_000741215.1", "gtdb_species": "s__Bifidobacterium pullorum_B", "ani": 79.4238, "matched_fragments": 304, "total_fragments": 902, "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", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_009299505.1", "gtdb_species": "s__Bifidobacterium ramosum", "ani": 79.4058, "matched_fragments": 317, "total_fragments": 902, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009299475.1", "gtdb_species": "s__Bifidobacterium avesanii", "ani": 79.3381, "matched_fragments": 292, "total_fragments": 902, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018555335.1", "gtdb_species": "s__Bifidobacterium sp018555335", "ani": 79.3339, "matched_fragments": 301, "total_fragments": 902, "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_018555355.1", "gtdb_species": "s__Bifidobacterium sp018555355", "ani": 79.2572, "matched_fragments": 305, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.26", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000741165.1", "gtdb_species": "s__Bifidobacterium biavatii", "ani": 79.1473, "matched_fragments": 307, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009078285.1", "gtdb_species": "s__Bifidobacterium jacchi", "ani": 78.9134, "matched_fragments": 274, "total_fragments": 902, "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_002860355.1", "gtdb_species": "s__Galliscardovia margollesii", "ani": 78.812, "matched_fragments": 225, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Galliscardovia", "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_000771225.1", "gtdb_species": "s__Bifidobacterium pseudolongum", "ani": 78.5671, "matched_fragments": 227, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 10, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.301, "doubling_h": 0.178, "growth_tmp": 37.0, "optimum_tmp": 34.75, "optimum_ph": 6.377, "genome_size": 2773540.0, "gc_content": 60.9, "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", "subtile", "DSM", "20096" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }