{ "type": "genome", "identifier": "GCF_000296405.1", "organism": "Corynebacterium otitidis ATCC 51513", "title": "Corynebacterium otitidis ATCC 51513", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000296405.1", "bioproject": "PRJNA224116", "biosample": "SAMN02463914", "wgs_master": "AHAE00000000.1", "refseq_category": "reference genome", "taxid": "883169", "species_taxid": "29321", "organism_name": "Corynebacterium otitidis ATCC 51513", "infraspecific_name": "strain=ATCC 51513", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/09/17", "asm_name": "Turi_otit_ATCC_51513_V1", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000296405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/296/405/GCF_000296405.1_Turi_otit_ATCC_51513_V1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2118285", "genome_size_ungapped": "2090523", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "87", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000296405.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "1883", "protein_coding_gene_count": "1777", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-09-17", "dateModified": "2012-09-17", "datePublished": "2012-09-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Corynebacterium otitidis ATCC 51513" ], "sample_taxid": [ "883169" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "0.558 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.54, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2118285", "Number of Sequences": "6", "Longest Sequences (bp)": "659597", "N50 (bp)": "595073", "Gap Ratio (%)": "1.310589", "GCcontent (%)": "71.4", "Number of CDSs": "1808", "Average Protein Length": "334.1", "Coding Ratio (%)": "85.5", "Number of rRNAs": "2", "Number of tRNAs": "58", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Corynebacterium otitidis", "strain": "strain=ATCC 51513", "accession": "GCA_000296405.1", "taxid": 29321, "species_taxid": 29321, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 703, "total_fragments": 703, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Corynebacterium otitidis", "strain": "strain=ATCC 51513", "accession": "GCA_000297795.2", "taxid": 29321, "species_taxid": 29321, "relation_to_type": "type", "validated": true, "ani": 99.8334, "matched_fragments": 699, "total_fragments": 703, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Corynebacterium frankenforstense", "strain": "strain=ST18", "accession": "GCA_001941485.1", "taxid": 1230998, "species_taxid": 1230998, "relation_to_type": "type", "validated": true, "ani": 79.9712, "matched_fragments": 387, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium halotolerans", "strain": "strain=YIM 70093 = DSM 44683", "accession": "GCA_000341345.1", "taxid": 225326, "species_taxid": 225326, "relation_to_type": "type", "validated": true, "ani": 78.9344, "matched_fragments": 329, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium halotolerans", "strain": "strain=DSM 44683", "accession": "GCA_000688435.1", "taxid": 225326, "species_taxid": 225326, "relation_to_type": "type", "validated": true, "ani": 78.8286, "matched_fragments": 323, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium vitaeruminis", "strain": "strain=DSM 20294", "accession": "GCA_000550805.1", "taxid": 38305, "species_taxid": 38305, "relation_to_type": "type", "validated": true, "ani": 78.7892, "matched_fragments": 299, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium pollutisoli", "strain": "strain=VDS11", "accession": "GCA_900177745.1", "taxid": 1610489, "species_taxid": 1610489, "relation_to_type": "type", "validated": true, "ani": 78.6619, "matched_fragments": 316, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium humireducens", "strain": "strain=DSM 45392", "accession": "GCA_000819445.1", "taxid": 1223514, "species_taxid": 1223514, "relation_to_type": "type", "validated": true, "ani": 78.5638, "matched_fragments": 310, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium jeddahense", "strain": "strain=JCB", "accession": "GCA_000577555.1", "taxid": 1414719, "species_taxid": 1414719, "relation_to_type": "type", "validated": true, "ani": 78.4941, "matched_fragments": 273, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium mastitidis", "strain": "strain=DSM 44356", "accession": "GCA_000375365.1", "taxid": 161890, "species_taxid": 161890, "relation_to_type": "type", "validated": true, "ani": 78.4668, "matched_fragments": 286, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium humireducens", "strain": "strain=NBRC 106098", "accession": "GCA_001571025.1", "taxid": 1223514, "species_taxid": 1223514, "relation_to_type": "type", "validated": true, "ani": 78.4569, "matched_fragments": 306, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium massiliense", "strain": "strain=DSM 45435", "accession": "GCA_000420605.1", "taxid": 441501, "species_taxid": 441501, "relation_to_type": "type", "validated": true, "ani": 78.2113, "matched_fragments": 209, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces varsoviensis", "strain": "strain=NRRL B-3589", "accession": "GCA_000719255.1", "taxid": 67373, "species_taxid": 67373, "relation_to_type": "type", "validated": true, "ani": 75.8742, "matched_fragments": 235, "total_fragments": 703, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.54, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000296405.1", "gtdb_species": "s__Corynebacterium otitidis", "ani": 99.9999, "matched_fragments": 703, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001941485.1", "gtdb_species": "s__Corynebacterium frankenforstense", "ani": 79.9062, "matched_fragments": 389, "total_fragments": 703, "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_000341345.1", "gtdb_species": "s__Corynebacterium halotolerans", "ani": 78.9517, "matched_fragments": 331, "total_fragments": 703, "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_000550805.1", "gtdb_species": "s__Corynebacterium vitaeruminis", "ani": 78.7566, "matched_fragments": 301, "total_fragments": 703, "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_900177745.1", "gtdb_species": "s__Corynebacterium pollutisoli", "ani": 78.6155, "matched_fragments": 320, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.83", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000819445.1", "gtdb_species": "s__Corynebacterium humireducens", "ani": 78.5495, "matched_fragments": 311, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "97.60", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000577555.1", "gtdb_species": "s__Corynebacterium jeddahense", "ani": 78.545, "matched_fragments": 270, "total_fragments": 703, "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_000375365.1", "gtdb_species": "s__Corynebacterium mastitidis", "ani": 78.4751, "matched_fragments": 286, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "96.64", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014267345.1", "gtdb_species": "s__Corynebacterium sp014267345", "ani": 78.0485, "matched_fragments": 196, "total_fragments": 703, "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": "GCA_012838985.1", "gtdb_species": "s__Corynebacterium sp012838985", "ani": 77.9138, "matched_fragments": 265, "total_fragments": 703, "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_001482365.1", "gtdb_species": "s__Kocuria flava", "ani": 76.4275, "matched_fragments": 200, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000718635.1", "gtdb_species": "s__Streptomyces varsoviensis", "ani": 75.7684, "matched_fragments": 237, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_004005495.1", "gtdb_species": "s__Streptomyces sp004005495", "ani": 75.7023, "matched_fragments": 225, "total_fragments": 703, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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": -0.275, "cell_length": 0.068, "doubling_h": -0.089, "growth_tmp": 35.111, "optimum_tmp": 35.173, "optimum_ph": 7.292, "genome_size": 2639223.511, "gc_content": 59.791, "coding_genes": 2390.094, "rRNA16S_genes": 4.282, "tRNA_genes": 52.979, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.75, "facultative_respiration": 0.231, "anaerobic_respiration": 0.063, "aerobic_respiration": 0.705, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.985, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.014, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Corynebacterium", "otitidis", "ATCC", "51513" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }