{ "type": "genome", "identifier": "GCF_001457455.1", "organism": "Corynebacterium diphtheriae", "title": "Corynebacterium diphtheriae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001457455.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2517360", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1717", "species_taxid": "1717", "organism_name": "Corynebacterium diphtheriae", "infraspecific_name": "strain=NCTC11397", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/03/22", "asm_name": "NCTC11397", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_001457455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/457/455/GCF_001457455.1_NCTC11397", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2463666", "genome_size_ungapped": "2463666", "gc_percent": "53.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001457455.1-RS_2024_03_30", "annotation_date": "2024-03-30", "total_gene_count": "2372", "protein_coding_gene_count": "2220", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-03-22", "dateModified": "2015-03-22", "datePublished": "2015-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Corynebacterium diphtheriae" ], "sample_taxid": [ "1717" ], "sample_host_organism": [ "unknown" ], "sample_host_organism_id": [], "sample_host_disease": [ "not known", "not known" ], "sample_host_disease_id": [], "sample_host_location": [ "USA", "USA" ], "sample_host_location_id": [], "data_size": "0.703 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.54, "contamination": 1.56, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2463666", "Number of Sequences": "1", "Longest Sequences (bp)": "2463666", "N50 (bp)": "2463666", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.5", "Number of CDSs": "2316", "Average Protein Length": "309.3", "Coding Ratio (%)": "87.2", "Number of rRNAs": "15", "Number of tRNAs": "55", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Corynebacterium diphtheriae", "strain": "strain=NCTC11397", "accession": "GCA_001457455.1", "taxid": 1717, "species_taxid": 1717, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 818, "total_fragments": 821, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Corynebacterium diphtheriae", "strain": "", "accession": "GCA_902809765.1", "taxid": 1717, "species_taxid": 1717, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 818, "total_fragments": 821, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Corynebacterium diphtheriae subsp. diphtheriae", "strain": "strain=FDAARGOS_1554", "accession": "GCA_020736085.1", "taxid": 2315257, "species_taxid": 1717, "relation_to_type": "type", "validated": true, "ani": 99.9998, "matched_fragments": 817, "total_fragments": 821, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Corynebacterium diphtheriae", "strain": "strain=DSM 44123", "accession": "GCA_001913265.1", "taxid": 1717, "species_taxid": 1717, "relation_to_type": "type", "validated": true, "ani": 99.973, "matched_fragments": 775, "total_fragments": 821, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Corynebacterium belfantii", "strain": "", "accession": "GCA_900205605.1", "taxid": 2014537, "species_taxid": 2014537, "relation_to_type": "type", "validated": true, "ani": 95.083, "matched_fragments": 692, "total_fragments": 821, "ani_threshold": 95, "status": "inconclusive" } ], "cc_result": { "completeness": 99.54, "contamination": 1.56, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_001457455.1", "gtdb_species": "s__Corynebacterium diphtheriae", "ani": 100.0, "matched_fragments": 817, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 346, "status": "conclusive" }, { "accession": "GCF_902702935.1", "gtdb_species": "s__Corynebacterium rouxii", "ani": 92.7819, "matched_fragments": 708, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_900187135.1", "gtdb_species": "s__Corynebacterium ulcerans", "ani": 80.2101, "matched_fragments": 163, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 38, "status": "-" }, { "accession": "GCF_001054945.1", "gtdb_species": "s__Corynebacterium falsenii_A", "ani": 80.1796, "matched_fragments": 57, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_001941565.1", "gtdb_species": "s__Corynebacterium phocae", "ani": 79.5691, "matched_fragments": 63, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_002155265.1", "gtdb_species": "s__Corynebacterium pseudotuberculosis", "ani": 79.401, "matched_fragments": 162, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 131, "status": "-" }, { "accession": "GCF_000177535.2", "gtdb_species": "s__Corynebacterium resistens", "ani": 79.3116, "matched_fragments": 66, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_000550805.1", "gtdb_species": "s__Corynebacterium vitaeruminis", "ani": 79.1731, "matched_fragments": 143, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003814005.1", "gtdb_species": "s__Corynebacterium pseudopelargi", "ani": 79.1338, "matched_fragments": 123, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_001020985.1", "gtdb_species": "s__Corynebacterium mustelae", "ani": 79.0582, "matched_fragments": 90, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_004382825.2", "gtdb_species": "s__Corynebacterium silvaticum", "ani": 79.0203, "matched_fragments": 169, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.78", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_011612265.2", "gtdb_species": "s__Corynebacterium matruchotii", "ani": 78.992, "matched_fragments": 70, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "97.18", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001767255.1", "gtdb_species": "s__Corynebacterium sp001767255", "ani": 78.8128, "matched_fragments": 82, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.41", "min_intra_species_ani": "96.75", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004114895.1", "gtdb_species": "s__Corynebacterium pelargi", "ani": 78.7171, "matched_fragments": 133, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_014837045.1", "gtdb_species": "s__Corynebacterium sp014837045", "ani": 78.3794, "matched_fragments": 93, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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_003955685.1", "gtdb_species": "s__Corynebacterium sp003955685", "ani": 77.7818, "matched_fragments": 86, "total_fragments": 821, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": 0.0, "doubling_h": -0.247, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.292, "genome_size": 2452132.333, "gc_content": 53.54, "coding_genes": 2228.939, "rRNA16S_genes": 5.0, "tRNA_genes": 51.105, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.75, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Corynebacterium", "diphtheriae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }