{ "type": "genome", "identifier": "GCF_003254575.1", "organism": "Mycobacterium kyogaense", "title": "Mycobacterium kyogaense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Newcastle University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003254575.1", "bioproject": "PRJNA224116", "biosample": "SAMN09281965", "wgs_master": "QJUA00000000.1", "refseq_category": "reference genome", "taxid": "2212479", "species_taxid": "2212479", "organism_name": "Mycobacterium kyogaense", "infraspecific_name": "strain=NCTC 11659", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/18", "asm_name": "ASM325457v1", "asm_submitter": "Newcastle University", "gbrs_paired_asm": "GCA_003254575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/575/GCF_003254575.1_ASM325457v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5759757", "genome_size_ungapped": "5759757", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "132", "contig_count": "132", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003254575.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5597", "protein_coding_gene_count": "5444", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-18", "dateModified": "2018-06-18", "datePublished": "2018-06-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium kyogaense" ], "sample_taxid": [ "2212479" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Uganda" ], 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"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": 84.4785, "matched_fragments": 1378, "total_fragments": 1866, "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": 84.3, "matched_fragments": 1346, "total_fragments": 1866, "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": 84.2834, "matched_fragments": 1329, "total_fragments": 1866, "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": 84.2569, "matched_fragments": 1364, "total_fragments": 1866, "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": 84.1622, "matched_fragments": 1280, "total_fragments": 1866, "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": 80.063, "matched_fragments": 865, "total_fragments": 1866, "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": 79.8411, "matched_fragments": 819, "total_fragments": 1866, "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": 79.7316, "matched_fragments": 810, "total_fragments": 1866, "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": 79.7235, "matched_fragments": 838, "total_fragments": 1866, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fortuitum 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"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": 84.3143, "matched_fragments": 1362, "total_fragments": 1866, "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": 84.2989, "matched_fragments": 1326, "total_fragments": 1866, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 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"N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.117, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 34.928, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 5658460.823, "gc_content": 66.422, "coding_genes": 4941.245, "rRNA16S_genes": 1.504, "tRNA_genes": 48.184, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.2, "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": 0.842, "coccus_cell_shape": 0.057, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.1, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycobacterium", "kyogaense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }