{ "type": "genome", "identifier": "GCF_001044245.1", "organism": "Mycolicibacterium obuense", "title": "Mycolicibacterium obuense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001044245.1", "bioproject": "PRJNA224116", "biosample": "SAMN02952053", "wgs_master": "JYNU00000000.1", "refseq_category": "na", "taxid": "1807", "species_taxid": "1807", "organism_name": "Mycolicibacterium obuense", "infraspecific_name": "strain=DSM 44075", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/01", "asm_name": "ASM104424v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_001044245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/044/245/GCF_001044245.1_ASM104424v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5710643", "genome_size_ungapped": "5710643", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001044245.1-RS_2024_07_07", "annotation_date": "2024-07-07", "total_gene_count": "5582", "protein_coding_gene_count": "5369", "non_coding_gene_count": "54", "pubmed_id": "26079817" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-07-01", "dateModified": "2015-07-01", "datePublished": "2015-07-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacterium obuense" ], "sample_taxid": [ "1807" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.557 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)": "5710643", "Number of Sequences": "58", "Longest Sequences (bp)": "800070", "N50 (bp)": "215061", "Gap Ratio (%)": "0.002031", "GCcontent (%)": "68.0", "Number of CDSs": "5461", "Average Protein Length": "323.2", "Coding Ratio (%)": "92.7", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacterium chlorophenolicum", "strain": "strain=NBRC 15527", "accession": "GCA_001552315.1", "taxid": 37916, "species_taxid": 37916, "relation_to_type": "type", "validated": true, "ani": 84.5002, "matched_fragments": 1401, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium chlorophenolicum", "strain": "strain=DSM 43826", "accession": "GCA_001044235.1", "taxid": 37916, "species_taxid": 37916, "relation_to_type": "type", "validated": true, "ani": 84.4655, "matched_fragments": 1401, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=DSM 44219", "accession": "GCA_002086595.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 84.3706, "matched_fragments": 1353, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=DSM 44219", "accession": "GCA_001044255.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 84.3202, "matched_fragments": 1347, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=NCTC10819", "accession": "GCA_900453455.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 84.2749, "matched_fragments": 1400, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium psychrotolerans", "strain": "strain=JCM 13323", "accession": "GCA_010729305.1", "taxid": 216929, "species_taxid": 216929, "relation_to_type": "type", "validated": true, "ani": 84.2268, "matched_fragments": 1273, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium aurum", "strain": "strain=NCTC 10437", "accession": "GCA_001049355.1", "taxid": 1791, "species_taxid": 1791, "relation_to_type": "type", "validated": true, "ani": 81.1103, "matched_fragments": 1114, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium aurum", "strain": "strain=NCTC10437", "accession": "GCA_900637195.1", "taxid": 1791, "species_taxid": 1791, "relation_to_type": "type", "validated": true, "ani": 81.0588, "matched_fragments": 1131, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium rutilum", "strain": "strain=DSM 45405", "accession": "GCA_900108565.1", "taxid": 370526, "species_taxid": 370526, "relation_to_type": "type", "validated": true, "ani": 80.8928, "matched_fragments": 988, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium bacteremicum", "strain": "strain=DSM 45578", "accession": "GCA_002086115.1", "taxid": 564198, "species_taxid": 564198, "relation_to_type": "type", "validated": true, "ani": 80.0698, "matched_fragments": 893, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium pallens", "strain": "strain=JCM 16370", "accession": "GCA_019456675.1", "taxid": 370524, "species_taxid": 370524, "relation_to_type": "type", "validated": true, "ani": 79.8032, "matched_fragments": 832, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fortuitum subsp. fortuitum", "strain": "strain=JCM 6387", "accession": "GCA_022179545.1", "taxid": 144549, "species_taxid": 1766, "relation_to_type": "type", "validated": true, "ani": 79.7346, "matched_fragments": 794, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium crocinum", "strain": "strain=JCM 16369", "accession": "GCA_022370635.3", "taxid": 388459, "species_taxid": 388459, "relation_to_type": "type", "validated": true, "ani": 79.7036, "matched_fragments": 833, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium vinylchloridicum", "strain": "strain=CECT 8761", "accession": "GCA_013404075.1", "taxid": 2736928, "species_taxid": 2736928, "relation_to_type": "type", "validated": true, "ani": 79.6399, "matched_fragments": 791, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium anyangense", "strain": "strain=JCM 30275", "accession": "GCA_010731855.1", "taxid": 1431246, "species_taxid": 1431246, "relation_to_type": "type", "validated": true, "ani": 79.6293, "matched_fragments": 829, "total_fragments": 1879, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001044245.1", "gtdb_species": "s__Mycobacterium obuense", "ani": 100.0, "matched_fragments": 1875, "total_fragments": 1879, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "96.27", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_007096635.1", "gtdb_species": "s__Mycobacterium sp007096635", "ani": 87.0676, "matched_fragments": 1463, "total_fragments": 1879, "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_001044235.1", "gtdb_species": "s__Mycobacterium chlorophenolicum", "ani": 84.447, "matched_fragments": 1406, "total_fragments": 1879, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.8643, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "97.93", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_000762985.1", "gtdb_species": "s__Mycobacterium rufum_A", "ani": 84.3607, "matched_fragments": 1372, "total_fragments": 1879, "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_001044255.1", "gtdb_species": "s__Mycobacterium chubuense", "ani": 84.3424, "matched_fragments": 1344, "total_fragments": 1879, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.8643, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_010729305.1", "gtdb_species": "s__Mycobacterium psychrotolerans", "ani": 84.2298, "matched_fragments": 1274, "total_fragments": 1879, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.53", "min_intra_species_ani": "96.53", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000266905.1", "gtdb_species": "s__Mycobacterium chubuense_A", "ani": 82.0907, "matched_fragments": 1155, "total_fragments": 1879, "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_001545925.1", "gtdb_species": "s__Mycobacterium sp001545925", "ani": 81.8247, "matched_fragments": 912, "total_fragments": 1879, "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_014190915.1", "gtdb_species": "s__Mycobacterium iranicum_B", "ani": 81.6293, "matched_fragments": 1092, "total_fragments": 1879, "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_010723735.1", "gtdb_species": "s__Mycobacterium hippocampi_B", "ani": 81.3638, "matched_fragments": 1031, "total_fragments": 1879, "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_900108565.1", "gtdb_species": "s__Mycobacterium rutilum", "ani": 80.9051, "matched_fragments": 985, "total_fragments": 1879, "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_002086115.1", "gtdb_species": "s__Mycobacterium bacteremicum", "ani": 80.0452, "matched_fragments": 897, "total_fragments": 1879, "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_001494595.1", "gtdb_species": "s__Mycobacterium sp001494595", "ani": 79.859, "matched_fragments": 855, "total_fragments": 1879, "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_010731855.1", "gtdb_species": "s__Mycobacterium anyangense", "ani": 79.6219, "matched_fragments": 830, "total_fragments": 1879, "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_004362315.1", "gtdb_species": "s__Mycobacterium sp004362315", "ani": 79.5716, "matched_fragments": 868, "total_fragments": 1879, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 6, "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": [ "Mycolicibacterium", "obuense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }