{ "type": "genome", "identifier": "GCF_001552715.1", "organism": "Mycolicibacterium vaccae NBRC 14118 = CIP 105934", "title": "Mycolicibacterium vaccae NBRC 14118 = CIP 105934", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001552715.1", "bioproject": "PRJNA224116", "biosample": "SAMD00046508", "wgs_master": "BCRS00000000.1", "refseq_category": "na", "taxid": "1223499", "species_taxid": "1810", "organism_name": "Mycolicibacterium vaccae NBRC 14118 = CIP 105934", "infraspecific_name": "strain=NBRC 14118", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/02/06", "asm_name": "ASM155271v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_001552715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/552/715/GCF_001552715.1_ASM155271v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6168821", "genome_size_ungapped": "6168821", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "370", "contig_count": "370", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001552715.1-RS_2024_07_07", "annotation_date": "2024-07-07", "total_gene_count": "6163", "protein_coding_gene_count": "5872", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-02-06", "dateModified": "2016-02-06", "datePublished": "2016-02-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacterium vaccae NBRC 14118 = CIP 105934" ], "sample_taxid": [ "1223499" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.687 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)": "6168821", "Number of Sequences": "370", "Longest Sequences (bp)": "130283", "N50 (bp)": "30126", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.6", "Number of CDSs": "5588", "Average Protein Length": "317.6", "Coding Ratio (%)": "86.3", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacterium vaccae", "strain": "strain=NBRC 14118", "accession": "GCA_001552715.1", "taxid": 1810, "species_taxid": 1810, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1859, "total_fragments": 1870, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycolicibacterium vaccae", "strain": "strain=95051", "accession": "GCA_001655245.1", "taxid": 1810, "species_taxid": 1810, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 1869, "total_fragments": 1870, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=DSM 44219", "accession": "GCA_002086595.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 82.8387, "matched_fragments": 1160, "total_fragments": 1870, "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": 82.8079, "matched_fragments": 1155, "total_fragments": 1870, "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": 82.8071, "matched_fragments": 1183, "total_fragments": 1870, "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": 82.8014, "matched_fragments": 1172, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium chlorophenolicum", "strain": "strain=NBRC 15527", "accession": "GCA_001552315.1", "taxid": 37916, "species_taxid": 37916, "relation_to_type": "type", "validated": true, "ani": 82.7549, "matched_fragments": 1187, "total_fragments": 1870, "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": 82.6064, "matched_fragments": 1224, "total_fragments": 1870, "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": 82.5627, "matched_fragments": 1233, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium litorale", "strain": "strain=JCM 17423", "accession": "GCA_010731695.1", "taxid": 758802, "species_taxid": 758802, "relation_to_type": "type", "validated": true, "ani": 81.2782, "matched_fragments": 1047, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium litorale", "strain": "strain=CGMCC 4.5724", "accession": "GCA_004366555.1", "taxid": 758802, "species_taxid": 758802, "relation_to_type": "type", "validated": true, "ani": 81.226, "matched_fragments": 1048, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium aquaticum", "strain": "strain=RW6", "accession": "GCA_002086485.1", "taxid": 1927124, "species_taxid": 1927124, "relation_to_type": "type", "validated": true, "ani": 80.2807, "matched_fragments": 893, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium mageritense", "strain": "strain=JCM 12375", "accession": "GCA_010727475.1", "taxid": 53462, "species_taxid": 53462, "relation_to_type": "type", "validated": true, "ani": 80.279, "matched_fragments": 950, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium mageritense", "strain": "strain=CIP 104973", "accession": "GCA_000612825.1", "taxid": 53462, "species_taxid": 53462, "relation_to_type": "type", "validated": true, "ani": 80.275, "matched_fragments": 954, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium dioxanotrophicus", "strain": "strain=PH-06", "accession": "GCA_002157835.1", "taxid": 482462, "species_taxid": 482462, "relation_to_type": "type", "validated": true, "ani": 80.2285, "matched_fragments": 910, "total_fragments": 1870, "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": 80.167, "matched_fragments": 899, "total_fragments": 1870, "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": 80.1418, "matched_fragments": 765, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fortuitum subsp. acetamidolyticum", "strain": "strain=JCM6368", "accession": "GCA_001570465.1", "taxid": 144550, "species_taxid": 1766, "relation_to_type": "type", "validated": true, "ani": 80.0636, "matched_fragments": 898, "total_fragments": 1870, "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": 80.0087, "matched_fragments": 833, "total_fragments": 1870, "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": 79.998, "matched_fragments": 842, "total_fragments": 1870, "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": 79.9653, "matched_fragments": 801, "total_fragments": 1870, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001552715.1", "gtdb_species": "s__Mycobacterium vaccae", "ani": 100.0, "matched_fragments": 1859, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001545925.1", "gtdb_species": "s__Mycobacterium sp001545925", "ani": 86.3111, "matched_fragments": 1178, "total_fragments": 1870, "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_000612725.1", "gtdb_species": "s__Mycobacterium austroafricanum", "ani": 85.0487, "matched_fragments": 1285, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002086815.1", "gtdb_species": "s__Mycobacterium parafortuitum", "ani": 83.8983, "matched_fragments": 1343, "total_fragments": 1870, "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_010725485.1", "gtdb_species": "s__Mycobacterium sp002946335", "ani": 83.7357, "matched_fragments": 1333, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900454025.1", "gtdb_species": "s__Mycobacterium gilvum", "ani": 83.4851, "matched_fragments": 1211, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_014190915.1", "gtdb_species": "s__Mycobacterium iranicum_B", "ani": 82.9022, "matched_fragments": 1200, "total_fragments": 1870, "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": 82.8303, "matched_fragments": 1181, "total_fragments": 1870, "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": "GCF_010726645.1", "gtdb_species": "s__Mycobacterium duvalii", "ani": 82.492, "matched_fragments": 1072, "total_fragments": 1870, "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_010731695.1", "gtdb_species": "s__Mycobacterium litorale", "ani": 81.2812, "matched_fragments": 1048, "total_fragments": 1870, "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_001907655.1", "gtdb_species": "s__Mycobacterium diernhoferi", "ani": 81.1338, "matched_fragments": 1034, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.94", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001457595.1", "gtdb_species": "s__Mycobacterium smegmatis", "ani": 80.7129, "matched_fragments": 1036, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.06", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCF_002086835.1", "gtdb_species": "s__Mycobacterium porcinum", "ani": 80.5184, "matched_fragments": 949, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "97.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_010727475.1", "gtdb_species": "s__Mycobacterium mageritense", "ani": 80.2604, "matched_fragments": 953, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000295855.1", "gtdb_species": "s__Mycobacterium fortuitum", "ani": 80.1876, "matched_fragments": 886, "total_fragments": 1870, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "96.41", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 30, "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", "vaccae", "NBRC", "14118", "=", "CIP", "105934" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }