{ "type": "genome", "identifier": "GCF_900078685.2", "organism": "Mycolicibacter icosiumassiliensis", "title": "Mycolicibacter icosiumassiliensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900078685.2", "bioproject": "PRJNA224116", "biosample": "SAMEA3913389", "wgs_master": "FJVP00000000.1", "refseq_category": "reference genome", "taxid": "1792835", "species_taxid": "1792835", "organism_name": "Mycolicibacter icosiumassiliensis", "infraspecific_name": "strain=8WA6", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/04/02", "asm_name": "PRJEB13234", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900078685.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/078/685/GCF_900078685.2_PRJEB13234", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4849907", "genome_size_ungapped": "4844630", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "42", "contig_count": "79", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900078685.2-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4762", "protein_coding_gene_count": "4426", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-04-02", "dateModified": "2016-04-02", "datePublished": "2016-04-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacter icosiumassiliensis" ], "sample_taxid": [ "1792835" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.329 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)": "4849907", "Number of Sequences": "42", "Longest Sequences (bp)": "3843338", "N50 (bp)": "3843338", "Gap Ratio (%)": "0.109445", "GCcontent (%)": "66.8", "Number of CDSs": "4690", "Average Protein Length": "310.7", "Coding Ratio (%)": "90.1", "Number of rRNAs": "12", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacter nonchromogenicus", "strain": "strain=DSM 44164", "accession": "GCA_002101775.1", "taxid": 1782, "species_taxid": 1782, "relation_to_type": "type", "validated": true, "ani": 88.4747, "matched_fragments": 1108, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter longobardus", "strain": "strain=DSM 45394", "accession": "GCA_002102265.1", "taxid": 1108812, "species_taxid": 1108812, "relation_to_type": "type", "validated": true, "ani": 86.431, "matched_fragments": 1119, "total_fragments": 1595, "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": 86.0282, "matched_fragments": 1080, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter minnesotensis", "strain": "strain=JCM 17932", "accession": "GCA_010731755.1", "taxid": 1118379, "species_taxid": 1118379, "relation_to_type": "type", "validated": true, "ani": 85.9529, "matched_fragments": 1125, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter hiberniae", "strain": "strain=ATCC 49874", "accession": "GCA_002101655.1", "taxid": 29314, "species_taxid": 29314, "relation_to_type": "type", "validated": true, "ani": 85.9033, "matched_fragments": 1080, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter hiberniae", "strain": "strain=JCM 13571", "accession": "GCA_010729485.1", "taxid": 29314, "species_taxid": 29314, "relation_to_type": "type", "validated": true, "ani": 85.8171, "matched_fragments": 1107, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter minnesotensis", "strain": "strain=DSM 45633", "accession": "GCA_002086405.1", "taxid": 1118379, "species_taxid": 1118379, "relation_to_type": "type", "validated": true, "ani": 85.81, "matched_fragments": 1095, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter arupensis", "strain": "strain=DSM 44942", "accession": "GCA_002086515.1", "taxid": 342002, "species_taxid": 342002, "relation_to_type": "type", "validated": true, "ani": 85.7605, "matched_fragments": 1111, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=CST 7247", "accession": "GCA_010093495.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 85.1265, "matched_fragments": 1030, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=DSM 45093", "accession": "GCA_002086285.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 85.0838, "matched_fragments": 1088, "total_fragments": 1595, "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": 84.5993, "matched_fragments": 1095, "total_fragments": 1595, "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": 84.5265, "matched_fragments": 1079, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium palustre", "strain": "strain=DSM 44572", "accession": "GCA_002101785.1", "taxid": 153971, "species_taxid": 153971, "relation_to_type": "type", "validated": true, "ani": 79.8381, "matched_fragments": 678, "total_fragments": 1595, "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": 79.3393, "matched_fragments": 636, "total_fragments": 1595, "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": 79.1599, "matched_fragments": 612, "total_fragments": 1595, "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": 79.1085, "matched_fragments": 622, "total_fragments": 1595, "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": 78.7887, "matched_fragments": 635, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium stellerae", "strain": "strain=CECT 8783", "accession": "GCA_003719305.1", "taxid": 2358193, "species_taxid": 2358193, "relation_to_type": "type", "validated": true, "ani": 78.6014, "matched_fragments": 540, "total_fragments": 1595, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900078685.2", "gtdb_species": "s__Mycobacterium icosiumassiliensis", "ani": 100.0, "matched_fragments": 1590, "total_fragments": 1595, "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": "conclusive" }, { "accession": "GCF_001673105.1", "gtdb_species": "s__Mycobacterium heraklionense_A", "ani": 90.4911, "matched_fragments": 1207, "total_fragments": 1595, "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_001021505.1", "gtdb_species": "s__Mycobacterium heraklionense_B", "ani": 90.1651, "matched_fragments": 1227, "total_fragments": 1595, "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_000455125.1", "gtdb_species": "s__Mycobacterium sp000455125", "ani": 89.798, "matched_fragments": 1150, "total_fragments": 1595, "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": 88.4961, "matched_fragments": 1106, "total_fragments": 1595, "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": 86.0459, "matched_fragments": 1079, "total_fragments": 1595, "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": "-" }, { "accession": "GCF_010731755.1", "gtdb_species": "s__Mycobacterium minnesotense", "ani": 85.9565, "matched_fragments": 1125, "total_fragments": 1595, "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_010729485.1", "gtdb_species": "s__Mycobacterium hiberniae", "ani": 85.8429, "matched_fragments": 1104, "total_fragments": 1595, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.4017, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "95.62", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002086515.1", "gtdb_species": "s__Mycobacterium arupense", "ani": 85.77, "matched_fragments": 1110, "total_fragments": 1595, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_002086285.1", "gtdb_species": "s__Mycobacterium kumamotonense", "ani": 85.1056, "matched_fragments": 1086, "total_fragments": 1595, "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": "-" }, { "accession": "GCF_001667945.1", "gtdb_species": "s__Mycobacterium sinense_B", "ani": 84.9917, "matched_fragments": 1068, "total_fragments": 1595, "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_002086455.1", "gtdb_species": "s__Mycobacterium algericum", "ani": 84.6756, "matched_fragments": 1054, "total_fragments": 1595, "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_018455725.1", "gtdb_species": "s__Mycobacterium sp018455725", "ani": 82.389, "matched_fragments": 931, "total_fragments": 1595, "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_011694515.1", "gtdb_species": "s__Mycobacterium sp011694515", "ani": 79.3736, "matched_fragments": 628, "total_fragments": 1595, "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_001245615.1", "gtdb_species": "s__Mycobacterium neworleansense", "ani": 79.2842, "matched_fragments": 659, "total_fragments": 1595, "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_013390125.1", "gtdb_species": "s__Mycobacterium hippocampi_A", "ani": 78.5559, "matched_fragments": 562, "total_fragments": 1595, "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": "-" } ] }, "_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", "icosiumassiliensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }