{ "type": "genome", "identifier": "GCF_010093495.1", "organism": "Mycolicibacter kumamotonensis", "title": "Mycolicibacter kumamotonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Instituto Politecnico Nacional", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010093495.1", "bioproject": "PRJNA224116", "biosample": "SAMN13905685", "wgs_master": "JAACYR000000000.1", "refseq_category": "na", "taxid": "354243", "species_taxid": "354243", "organism_name": "Mycolicibacter kumamotonensis", "infraspecific_name": "strain=CST 7247", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/03", "asm_name": "ASM1009349v1", "asm_submitter": "Instituto Politecnico Nacional", "gbrs_paired_asm": "GCA_010093495.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/093/495/GCF_010093495.1_ASM1009349v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4837841", "genome_size_ungapped": "4836621", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "260", "contig_count": "260", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010093495.1-RS_2024_08_06", "annotation_date": "2024-08-06", "total_gene_count": "4819", "protein_coding_gene_count": "4539", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-03", "dateModified": "2020-02-03", "datePublished": "2020-02-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacter kumamotonensis" ], "sample_taxid": [ "354243" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "mycobacteriosis" ], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.338 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)": "4837841", "Number of Sequences": "260", "Longest Sequences (bp)": "124932", "N50 (bp)": "46656", "Gap Ratio (%)": "0.026231", "GCcontent (%)": "68.1", "Number of CDSs": "4512", "Average Protein Length": "315.8", "Coding Ratio (%)": "88.4", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=CST 7247", "accession": "GCA_010093495.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1499, "total_fragments": 1510, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=DSM 45093", "accession": "GCA_002086285.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 98.5274, "matched_fragments": 1309, "total_fragments": 1510, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycolicibacter terrae", "strain": "strain=JCM 12143", "accession": "GCA_010727125.1", "taxid": 1788, "species_taxid": 1788, "relation_to_type": "type", "validated": true, "ani": 91.089, "matched_fragments": 1276, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter terrae", "strain": "strain=CIP 104321", "accession": "GCA_002101955.1", "taxid": 1788, "species_taxid": 1788, "relation_to_type": "type", "validated": true, "ani": 91.0638, "matched_fragments": 1262, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter senuensis", "strain": "strain=JCM 16017", "accession": "GCA_010723225.1", "taxid": 386913, "species_taxid": 386913, "relation_to_type": "type", "validated": true, "ani": 87.3283, "matched_fragments": 1177, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter senuensis", "strain": "strain=DSM 44999", "accession": "GCA_002101885.1", "taxid": 386913, "species_taxid": 386913, "relation_to_type": "type", "validated": true, "ani": 87.3248, "matched_fragments": 1163, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter nonchromogenicus", "strain": "strain=DSM 44164", "accession": "GCA_002101775.1", "taxid": 1782, "species_taxid": 1782, "relation_to_type": "type", "validated": true, "ani": 84.7741, "matched_fragments": 1063, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter engbaekii", "strain": "strain=ATCC 27353", "accession": "GCA_002101585.1", "taxid": 188915, "species_taxid": 188915, "relation_to_type": "type", "validated": true, "ani": 84.2296, "matched_fragments": 1064, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium branderi", "strain": "strain=JCM 12687", "accession": "GCA_010728725.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 80.1795, "matched_fragments": 792, "total_fragments": 1510, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002086285.1", "gtdb_species": "s__Mycobacterium kumamotonense", "ani": 98.5274, "matched_fragments": 1309, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_010727125.1", "gtdb_species": "s__Mycobacterium terrae", "ani": 91.0836, "matched_fragments": 1276, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001667375.1", "gtdb_species": "s__Mycobacterium sinense_A", "ani": 89.0422, "matched_fragments": 1163, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.51", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001667945.1", "gtdb_species": "s__Mycobacterium sinense_B", "ani": 88.9141, "matched_fragments": 1171, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.61", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003284925.1", "gtdb_species": "s__Mycobacterium algericum_A", "ani": 88.2105, "matched_fragments": 1122, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_002086455.1", "gtdb_species": "s__Mycobacterium algericum", "ani": 87.3419, "matched_fragments": 1173, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002101885.1", "gtdb_species": "s__Mycobacterium senuense", "ani": 87.3355, "matched_fragments": 1162, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_001021505.1", "gtdb_species": "s__Mycobacterium heraklionense_B", "ani": 85.5537, "matched_fragments": 1124, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_900078685.2", "gtdb_species": "s__Mycobacterium icosiumassiliensis", "ani": 85.0245, "matched_fragments": 1058, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "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_001673105.1", "gtdb_species": "s__Mycobacterium heraklionense_A", "ani": 85.0196, "matched_fragments": 1131, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.02", "min_intra_species_ani": "95.09", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000455125.1", "gtdb_species": "s__Mycobacterium sp000455125", "ani": 84.978, "matched_fragments": 1092, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002101775.1", "gtdb_species": "s__Mycobacterium nonchromogenicum", "ani": 84.7791, "matched_fragments": 1062, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.25", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002101585.1", "gtdb_species": "s__Mycobacterium engbaekii", "ani": 84.2402, "matched_fragments": 1064, "total_fragments": 1510, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.4017, "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Mycolicibacter", "kumamotonensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }