{ "type": "genome", "identifier": "GCF_002086595.1", "organism": "Mycolicibacterium chubuense", "title": "Mycolicibacterium chubuense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "San Raffaele Scientific Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002086595.1", "bioproject": "PRJNA224116", "biosample": "SAMN06064237", "wgs_master": "MVHO00000000.1", "refseq_category": "na", "taxid": "1800", "species_taxid": "1800", "organism_name": "Mycolicibacterium chubuense", "infraspecific_name": "strain=DSM 44219", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/11", "asm_name": "ASM208659v1", "asm_submitter": "San Raffaele Scientific Institute", "gbrs_paired_asm": "GCA_002086595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/086/595/GCF_002086595.1_ASM208659v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5946445", "genome_size_ungapped": "5946445", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "105", "contig_count": "105", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-11", "total_gene_count": "5748", "protein_coding_gene_count": "5610", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-11", "dateModified": "2017-04-11", "datePublished": "2017-04-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacterium chubuense" ], "sample_taxid": [ "1800" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.617 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 3.85, "strain_heterogeneity": 80.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5946445", "Number of Sequences": "105", "Longest Sequences (bp)": "534616", "N50 (bp)": "128197", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.2", "Number of CDSs": "5665", "Average Protein Length": "325.6", "Coding Ratio (%)": "93.1", "Number of rRNAs": "3", "Number of tRNAs": "59", "Number of CRISPRs": "8" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=DSM 44219", "accession": "GCA_002086595.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1942, "total_fragments": 1945, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=NCTC10819", "accession": "GCA_900453455.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 99.9924, "matched_fragments": 1942, "total_fragments": 1945, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium chubuense", "strain": "strain=DSM 44219", "accession": "GCA_001044255.1", "taxid": 1800, "species_taxid": 1800, "relation_to_type": "type", "validated": true, "ani": 99.9636, "matched_fragments": 1906, "total_fragments": 1945, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium chlorophenolicum", "strain": "strain=NBRC 15527", "accession": "GCA_001552315.1", "taxid": 37916, "species_taxid": 37916, "relation_to_type": "type", "validated": true, "ani": 95.8873, "matched_fragments": 1754, "total_fragments": 1945, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium chlorophenolicum", "strain": "strain=DSM 43826", "accession": "GCA_001044235.1", "taxid": 37916, "species_taxid": 37916, "relation_to_type": "type", "validated": true, "ani": 95.8796, "matched_fragments": 1767, "total_fragments": 1945, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium psychrotolerans", "strain": "strain=JCM 13323", "accession": "GCA_010729305.1", "taxid": 216929, "species_taxid": 216929, "relation_to_type": "type", "validated": true, "ani": 91.1295, "matched_fragments": 1594, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium arabiense", "strain": "strain=JCM 18538", "accession": "GCA_010731815.2", "taxid": 1286181, "species_taxid": 1286181, "relation_to_type": "type", "validated": true, "ani": 80.6719, "matched_fragments": 1075, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium lacusdiani", "strain": "strain=JXJ CY 35", "accession": "GCA_021916785.1", "taxid": 2895283, "species_taxid": 2895283, "relation_to_type": "type", "validated": true, "ani": 80.5375, "matched_fragments": 1081, "total_fragments": 1945, "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": 80.0701, "matched_fragments": 952, "total_fragments": 1945, "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": 79.9415, "matched_fragments": 947, "total_fragments": 1945, "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": 79.8837, "matched_fragments": 921, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant pinnipedii", "strain": "strain=ATCC BAA-688", "accession": "GCA_002982275.1", "taxid": 194542, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 78.1672, "matched_fragments": 503, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant microti", "strain": "strain=ATCC 19422", "accession": "GCA_002982215.1", "taxid": 1806, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 78.1501, "matched_fragments": 483, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant africanum", "strain": "strain=ATCC 25420", "accession": "GCA_002982335.1", "taxid": 33894, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 78.1201, "matched_fragments": 513, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant bovis", "strain": "strain=ATCC 19210", "accession": "GCA_002982285.1", "taxid": 1765, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 78.1019, "matched_fragments": 482, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis variant caprae", "strain": "strain=ATCC BAA-824", "accession": "GCA_002982225.1", "taxid": 115862, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 78.0803, "matched_fragments": 509, "total_fragments": 1945, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 3.85, "strain_heterogeneity": 80.0 }, "gtdb_result": [ { "accession": "GCF_001044255.1", "gtdb_species": "s__Mycobacterium chubuense", "ani": 99.9636, "matched_fragments": 1906, "total_fragments": 1945, "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": "inconclusive" }, { "accession": "GCF_001044235.1", "gtdb_species": "s__Mycobacterium chlorophenolicum", "ani": 95.8676, "matched_fragments": 1768, "total_fragments": 1945, "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": "inconclusive" }, { "accession": "GCF_010729305.1", "gtdb_species": "s__Mycobacterium psychrotolerans", "ani": 91.1352, "matched_fragments": 1593, "total_fragments": 1945, "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": "GCA_000762985.1", "gtdb_species": "s__Mycobacterium rufum_A", "ani": 89.2424, "matched_fragments": 1689, "total_fragments": 1945, "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_001044245.1", "gtdb_species": "s__Mycobacterium obuense", "ani": 84.1618, "matched_fragments": 1373, "total_fragments": 1945, "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": "-" }, { "accession": "GCF_007096635.1", "gtdb_species": "s__Mycobacterium sp007096635", "ani": 84.1085, "matched_fragments": 1322, "total_fragments": 1945, "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_004570325.1", "gtdb_species": "s__Mycobacterium sp004570325", "ani": 81.5738, "matched_fragments": 1090, "total_fragments": 1945, "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_010729665.1", "gtdb_species": "s__Mycobacterium madagascariense", "ani": 80.3533, "matched_fragments": 987, "total_fragments": 1945, "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_001673535.1", "gtdb_species": "s__Mycobacterium sp001673535", "ani": 79.5425, "matched_fragments": 780, "total_fragments": 1945, "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_001665295.1", "gtdb_species": "s__Mycobacterium sp001665295", "ani": 79.358, "matched_fragments": 802, "total_fragments": 1945, "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_000455205.1", "gtdb_species": "s__Mycobacterium sp000455205", "ani": 79.3368, "matched_fragments": 789, "total_fragments": 1945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.16", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000195955.2", "gtdb_species": "s__Mycobacterium tuberculosis", "ani": 78.0989, "matched_fragments": 527, "total_fragments": 1945, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.91", "num_clustered_genomes": 6836, "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", "chubuense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }