{ "type": "genome", "identifier": "GCF_022370635.2", "organism": "Mycolicibacterium crocinum", "title": "Mycolicibacterium crocinum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Institute of Tuberculosis", "publication": [ {} ], "properties": { "assembly_accession": "GCF_022370635.2", "bioproject": "PRJNA224116", "biosample": "SAMN20254251", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "388459", "species_taxid": "388459", "organism_name": "Mycolicibacterium crocinum", "infraspecific_name": "strain=JCM 16369", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/09/02", "asm_name": "ASM2237063v3", "asm_submitter": "Research Institute of Tuberculosis", "gbrs_paired_asm": "GCA_022370635.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/022/370/635/GCF_022370635.2_ASM2237063v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6183573", "genome_size_ungapped": "6183573", "gc_percent": "66.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_022370635.2-RS_2024_06_24", "annotation_date": "2024-06-24", "total_gene_count": "6073", "protein_coding_gene_count": "5912", "non_coding_gene_count": "55", "pubmed_id": "36651784" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-09-02", "dateModified": "2022-09-02", "datePublished": "2022-09-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacterium crocinum" ], "sample_taxid": [ "388459" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.696 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)": "6183573", "Number of Sequences": "3", "Longest Sequences (bp)": "5965857", "N50 (bp)": "5965857", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.6", "Number of CDSs": "6103", "Average Protein Length": "315.1", "Coding Ratio (%)": "93.3", "Number of rRNAs": "6", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium crocinum", "strain": "strain=JCM 16369", "accession": "GCA_022370635.3", "taxid": 388459, "species_taxid": 388459, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2060, "total_fragments": 2060, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycobacterium pallens", "strain": "strain=JCM 16370", "accession": "GCA_019456675.1", "taxid": 370524, "species_taxid": 370524, "relation_to_type": "type", "validated": true, "ani": 96.2081, "matched_fragments": 1796, "total_fragments": 2060, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium rhodesiae", "strain": "strain=DSM 44223", "accession": "GCA_002086695.1", "taxid": 36814, "species_taxid": 36814, "relation_to_type": "type", "validated": true, "ani": 86.8128, "matched_fragments": 1599, "total_fragments": 2060, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium aromaticivorans", "strain": "strain=JS19b1", "accession": "GCA_000559085.2", "taxid": 318425, "species_taxid": 318425, "relation_to_type": "type", "validated": true, "ani": 86.6954, "matched_fragments": 1631, "total_fragments": 2060, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium aichiense", "strain": "strain=NCTC10820", "accession": "GCA_900453085.1", "taxid": 1799, "species_taxid": 1799, "relation_to_type": "type", "validated": true, "ani": 86.6267, "matched_fragments": 1578, "total_fragments": 2060, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium aichiense", "strain": "strain=JCM 6376", "accession": "GCA_010726245.1", "taxid": 1799, "species_taxid": 1799, "relation_to_type": "type", "validated": true, "ani": 86.5895, "matched_fragments": 1585, "total_fragments": 2060, "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": 84.7399, "matched_fragments": 1527, "total_fragments": 2060, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium helvum", "strain": "strain=JCM 30396", "accession": "GCA_010731895.1", "taxid": 1534349, "species_taxid": 1534349, "relation_to_type": "type", "validated": true, "ani": 84.064, "matched_fragments": 1424, "total_fragments": 2060, "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": 82.0757, "matched_fragments": 1105, "total_fragments": 2060, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium baixiangningiae", "strain": "strain=LJ126", "accession": "GCA_014893035.1", "taxid": 2761578, "species_taxid": 2761578, "relation_to_type": "type", "validated": true, "ani": 79.5273, "matched_fragments": 853, "total_fragments": 2060, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001886515.1", "gtdb_species": "s__Mycobacterium sp001886515", "ani": 96.2908, "matched_fragments": 1777, "total_fragments": 2060, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001021385.1", "gtdb_species": "s__Mycobacterium sp001021385", "ani": 88.1332, "matched_fragments": 1670, "total_fragments": 2060, "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_008329565.1", "gtdb_species": "s__Mycobacterium sp008329565", "ani": 87.4413, "matched_fragments": 1500, "total_fragments": 2060, "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_002086695.1", "gtdb_species": "s__Mycobacterium rhodesiae", "ani": 86.8355, "matched_fragments": 1596, "total_fragments": 2060, "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_008329905.1", "gtdb_species": "s__Mycobacterium sp008329905", "ani": 86.7285, "matched_fragments": 1616, "total_fragments": 2060, "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_000559085.1", "gtdb_species": "s__Mycobacterium aromaticivorans", "ani": 86.682, "matched_fragments": 1635, "total_fragments": 2060, "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_010726245.1", "gtdb_species": "s__Mycobacterium aichiense", "ani": 86.5829, "matched_fragments": 1584, "total_fragments": 2060, "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_002887815.1", "gtdb_species": "s__Mycobacterium sp002887815", "ani": 86.5443, "matched_fragments": 1580, "total_fragments": 2060, "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": "GCA_900078375.1", "gtdb_species": "s__Mycobacterium sp900078375", "ani": 84.7944, "matched_fragments": 1495, "total_fragments": 2060, "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": "GCA_002007745.1", "gtdb_species": "s__Mycobacterium litorale_A", "ani": 82.761, "matched_fragments": 1263, "total_fragments": 2060, "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": [ "Mycolicibacterium", "crocinum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }