{ "type": "genome", "identifier": "GCF_022374895.2", "organism": "Mycobacterium lentiflavum", "title": "Mycobacterium lentiflavum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Institute of Tuberculosis", "publication": [ {} ], "properties": { "assembly_accession": "GCF_022374895.2", "bioproject": "PRJNA224116", "biosample": "SAMN20254258", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "141349", "species_taxid": "141349", "organism_name": "Mycobacterium lentiflavum", "infraspecific_name": "strain=ATCC 51985", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/08/24", "asm_name": "ASM2237489v2", "asm_submitter": "Research Institute of Tuberculosis", "gbrs_paired_asm": "GCA_022374895.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/022/374/895/GCF_022374895.2_ASM2237489v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6163560", "genome_size_ungapped": "6163560", "gc_percent": "66.000000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_022374895.2-RS_2024_06_24", "annotation_date": "2024-06-24", "total_gene_count": "5740", "protein_coding_gene_count": "5553", "non_coding_gene_count": "53", "pubmed_id": "36651784" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-08-24", "dateModified": "2022-08-24", "datePublished": "2022-08-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium lentiflavum" ], "sample_taxid": [ "141349" ], "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": "1.701 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6163560", "Number of Sequences": "4", "Longest Sequences (bp)": "5901783", "N50 (bp)": "5901783", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.9", "Number of CDSs": "5729", "Average Protein Length": "326.5", "Coding Ratio (%)": "91.0", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium lentiflavum", "strain": "strain=ATCC 51985", "accession": "GCA_022374895.2", "taxid": 141349, "species_taxid": 141349, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2051, "total_fragments": 2053, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium ahvazicum", "strain": "strain=AFP003", "accession": "GCA_900176255.2", "taxid": 1964395, "species_taxid": 1964395, "relation_to_type": "type", "validated": true, "ani": 91.6317, "matched_fragments": 1676, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium triplex", "strain": "strain=DSM 44626", "accession": "GCA_000689255.1", "taxid": 47839, "species_taxid": 47839, "relation_to_type": "type", "validated": true, "ani": 88.691, "matched_fragments": 1592, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium triplex", "strain": "strain=DSM 44626", "accession": "GCA_002102415.1", "taxid": 47839, "species_taxid": 47839, "relation_to_type": "type", "validated": true, "ani": 88.6591, "matched_fragments": 1579, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium florentinum", "strain": "strain=DSM 44852", "accession": "GCA_002101635.1", "taxid": 292462, "species_taxid": 292462, "relation_to_type": "type", "validated": true, "ani": 88.6314, "matched_fragments": 1580, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium florentinum", "strain": "strain=JCM 14740", "accession": "GCA_010730355.1", "taxid": 292462, "species_taxid": 292462, "relation_to_type": "type", "validated": true, "ani": 88.6161, "matched_fragments": 1591, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium stomatepiae", "strain": "strain=JCM 17783", "accession": "GCA_010731715.1", "taxid": 470076, "species_taxid": 470076, "relation_to_type": "type", "validated": true, "ani": 87.6487, "matched_fragments": 1557, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium genavense", "strain": "strain=ATCC 51234", "accession": "GCA_000526915.1", "taxid": 36812, "species_taxid": 36812, "relation_to_type": "type", "validated": true, "ani": 87.5104, "matched_fragments": 1371, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium simiae", "strain": "strain=JCM 12377", "accession": "GCA_010727605.1", "taxid": 1784, "species_taxid": 1784, "relation_to_type": "type", "validated": true, "ani": 83.2715, "matched_fragments": 1362, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium shigaense", "strain": "strain=UN-152", "accession": "GCA_002983495.1", "taxid": 722731, "species_taxid": 722731, "relation_to_type": "type", "validated": true, "ani": 82.8371, "matched_fragments": 1311, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium numidiamassiliense", "strain": "strain=AB215", "accession": "GCA_900157365.1", "taxid": 1841861, "species_taxid": 1841861, "relation_to_type": "type", "validated": true, "ani": 82.78, "matched_fragments": 1379, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium shigaense", "strain": "strain=JCM 32072", "accession": "GCA_002356315.1", "taxid": 722731, "species_taxid": 722731, "relation_to_type": "type", "validated": true, "ani": 82.7788, "matched_fragments": 1313, "total_fragments": 2053, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001373395.1", "gtdb_species": "s__Mycobacterium lentiflavum", "ani": 99.2216, "matched_fragments": 1917, "total_fragments": 2053, "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_900176255.2", "gtdb_species": "s__Mycobacterium ahvazicum", "ani": 91.6322, "matched_fragments": 1676, "total_fragments": 2053, "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_000689255.1", "gtdb_species": "s__Mycobacterium triplex", "ani": 88.6769, "matched_fragments": 1594, "total_fragments": 2053, "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": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010730355.1", "gtdb_species": "s__Mycobacterium florentinum", "ani": 88.6072, "matched_fragments": 1592, "total_fragments": 2053, "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_010731715.1", "gtdb_species": "s__Mycobacterium stomatepiae", "ani": 87.6461, "matched_fragments": 1557, "total_fragments": 2053, "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_000526915.1", "gtdb_species": "s__Mycobacterium genavense", "ani": 87.5198, "matched_fragments": 1370, "total_fragments": 2053, "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_003112775.1", "gtdb_species": "s__Mycobacterium montefiorense", "ani": 86.1976, "matched_fragments": 1475, "total_fragments": 2053, "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_900157375.1", "gtdb_species": "s__Mycobacterium rhizamassiliense", "ani": 83.3728, "matched_fragments": 1355, "total_fragments": 2053, "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_010727605.1", "gtdb_species": "s__Mycobacterium simiae", "ani": 83.2637, "matched_fragments": 1363, "total_fragments": 2053, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "97.21", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002356315.1", "gtdb_species": "s__Mycobacterium shigaense", "ani": 82.8121, "matched_fragments": 1308, "total_fragments": 2053, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.82", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900157365.1", "gtdb_species": "s__Mycobacterium numidiamassiliense", "ani": 82.7883, "matched_fragments": 1377, "total_fragments": 2053, "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": -0.117, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 37.0, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 6817509.0, "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", "lentiflavum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }