{ "type": "genome", "identifier": "GCF_025821985.1", "organism": "Mycobacterium timonense", "title": "Mycobacterium timonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025821985.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568982", "wgs_master": "JACKSY000000000.1", "refseq_category": "reference genome", "taxid": "701043", "species_taxid": "701043", "organism_name": "Mycobacterium timonense", "infraspecific_name": "strain=CCUG 56329", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582198v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025821985.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/821/985/GCF_025821985.1_ASM2582198v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5931282", "genome_size_ungapped": "5931282", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "119", "contig_count": "119", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025821985.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "5776", "protein_coding_gene_count": "5473", "non_coding_gene_count": "83", "pubmed_id": "36243697" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-10-24", "dateModified": "2022-10-24", "datePublished": "2022-10-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium timonense" ], "sample_taxid": [ "701043" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Marseille" ], "sample_host_location_id": [], "data_size": "1.621 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 30.0, "max": 30.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5931282", "Number of Sequences": "119", "Longest Sequences (bp)": "705490", "N50 (bp)": "170746", "Gap Ratio (%)": "0.001568", "GCcontent (%)": "68.6", "Number of CDSs": "5725", "Average Protein Length": "310.2", "Coding Ratio (%)": "89.8", "Number of rRNAs": "3", "Number of tRNAs": "86", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium avium subsp. avium", "strain": "strain=DSM 44156", "accession": "GCA_009741445.1", "taxid": 44454, "species_taxid": 1764, "relation_to_type": "type", "validated": true, "ani": 98.7639, "matched_fragments": 1533, "total_fragments": 1925, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium avium subsp. avium", "strain": "strain=ATCC 25291", "accession": "GCA_000174035.1", "taxid": 44454, "species_taxid": 1764, "relation_to_type": "type", "validated": true, "ani": 98.7304, "matched_fragments": 1394, "total_fragments": 1925, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium intracellulare", "strain": "strain=ATCC 13950", "accession": "GCA_023278525.1", "taxid": 1767, "species_taxid": 1767, "relation_to_type": "suspected-type", "validated": true, "ani": 87.455, "matched_fragments": 1427, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium intracellulare", "strain": "strain=ATCC 13950", "accession": "GCA_000277125.1", "taxid": 1767, "species_taxid": 1767, "relation_to_type": "suspected-type", "validated": true, "ani": 87.4331, "matched_fragments": 1429, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium intracellulare", "strain": "strain=ATCC 13950", "accession": "GCA_000172115.1", "taxid": 1767, "species_taxid": 1767, "relation_to_type": "suspected-type", "validated": true, "ani": 87.3249, "matched_fragments": 1271, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraintracellulare", "strain": "strain=JCM 30622", "accession": "GCA_010731935.1", "taxid": 1138383, "species_taxid": 1138383, "relation_to_type": "suspected-type", "validated": true, "ani": 87.3086, "matched_fragments": 1432, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraintracellulare", "strain": "strain=KCTC 29084", "accession": "GCA_002104735.1", "taxid": 1138383, "species_taxid": 1138383, "relation_to_type": "suspected-type", "validated": true, "ani": 87.2719, "matched_fragments": 1398, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraintracellulare", "strain": "strain=MOTT64", "accession": "GCA_000276825.1", "taxid": 1138383, "species_taxid": 1138383, "relation_to_type": "suspected-type", "validated": true, "ani": 87.2606, "matched_fragments": 1445, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium colombiense", "strain": "strain=CECT 3035", "accession": "GCA_002105755.1", "taxid": 339268, "species_taxid": 339268, "relation_to_type": "suspected-type", "validated": true, "ani": 87.1133, "matched_fragments": 1419, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium marseillense", "strain": "strain=JCM 17324", "accession": "GCA_010731675.1", "taxid": 701042, "species_taxid": 701042, "relation_to_type": "type", "validated": true, "ani": 87.0905, "matched_fragments": 1381, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium colombiense", "strain": "strain=CECT 3035", "accession": "GCA_000222105.4", "taxid": 339268, "species_taxid": 339268, "relation_to_type": "suspected-type", "validated": true, "ani": 87.0886, "matched_fragments": 1429, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium marseillense", "strain": "strain=DSM 45437", "accession": "GCA_002086345.1", "taxid": 701042, "species_taxid": 701042, "relation_to_type": "type", "validated": true, "ani": 87.0624, "matched_fragments": 1367, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium mantenii", "strain": "strain=JCM 18113", "accession": "GCA_010731775.1", "taxid": 560555, "species_taxid": 560555, "relation_to_type": "type", "validated": true, "ani": 86.6123, "matched_fragments": 1442, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium arosiense", "strain": "strain=DSM 45069", "accession": "GCA_002086125.1", "taxid": 425468, "species_taxid": 425468, "relation_to_type": "type", "validated": true, "ani": 86.1807, "matched_fragments": 1322, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium parmense", "strain": "strain=DSM 44553", "accession": "GCA_002102335.1", "taxid": 185642, "species_taxid": 185642, "relation_to_type": "type", "validated": true, "ani": 83.6574, "matched_fragments": 1250, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kyorinense", "strain": "strain=DSM 45166", "accession": "GCA_002101735.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 83.3417, "matched_fragments": 1084, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kyorinense", "strain": "strain=KUM060204T", "accession": "GCA_000759695.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 82.3883, "matched_fragments": 998, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium xenopi", "strain": "strain=NCTC10042", "accession": "GCA_900453395.1", "taxid": 1789, "species_taxid": 1789, "relation_to_type": "type", "validated": true, "ani": 81.1067, "matched_fragments": 964, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium fragae", "strain": "strain=DSM 45731", "accession": "GCA_002102185.1", "taxid": 1260918, "species_taxid": 1260918, "relation_to_type": "type", "validated": true, "ani": 80.9815, "matched_fragments": 955, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium xenopi", "strain": "strain=JCM 15661T", "accession": "GCA_009936235.1", "taxid": 1789, "species_taxid": 1789, "relation_to_type": "type", "validated": true, "ani": 80.6062, "matched_fragments": 922, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium xenopi", "strain": "strain=DSM 43995", "accession": "GCA_002102015.1", "taxid": 1789, "species_taxid": 1789, "relation_to_type": "type", "validated": true, "ani": 80.602, "matched_fragments": 909, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium heckeshornense", "strain": "strain=JCM 15655", "accession": "GCA_016592155.1", "taxid": 110505, "species_taxid": 110505, "relation_to_type": "type", "validated": true, "ani": 80.5518, "matched_fragments": 909, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium hassiacum", "strain": "strain=DSM 44199", "accession": "GCA_000379865.1", "taxid": 46351, "species_taxid": 46351, "relation_to_type": "type", "validated": true, "ani": 80.3608, "matched_fragments": 856, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium hassiacum", "strain": "strain=DSM 44199", "accession": "GCA_000300375.1", "taxid": 46351, "species_taxid": 46351, "relation_to_type": "type", "validated": true, "ani": 80.3323, "matched_fragments": 823, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium thermoresistibile", "strain": "strain=ATCC 19527", "accession": "GCA_000234585.2", "taxid": 1797, "species_taxid": 1797, "relation_to_type": "type", "validated": true, "ani": 80.2346, "matched_fragments": 795, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium thermoresistibile", "strain": "strain=NCTC10409", "accession": "GCA_900187065.1", "taxid": 1797, "species_taxid": 1797, "relation_to_type": "type", "validated": true, "ani": 80.1813, "matched_fragments": 814, "total_fragments": 1925, "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": 79.9545, "matched_fragments": 767, "total_fragments": 1925, "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": 79.4834, "matched_fragments": 759, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fortuitum subsp. fortuitum", "strain": "strain=DSM 46621", "accession": "GCA_000295855.1", "taxid": 144549, "species_taxid": 1766, "relation_to_type": "type", "validated": true, "ani": 79.468, "matched_fragments": 750, "total_fragments": 1925, "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": 79.3997, "matched_fragments": 813, "total_fragments": 1925, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009741445.1", "gtdb_species": "s__Mycobacterium avium", "ani": 98.7618, "matched_fragments": 1533, "total_fragments": 1925, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 96.9043, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.29", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 206, "status": "inconclusive" }, { "accession": "GCA_002291465.1", "gtdb_species": "s__Mycobacterium lepraemurium", "ani": 96.9321, "matched_fragments": 1297, "total_fragments": 1925, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 96.9043, "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": "inconclusive" }, { "accession": "GCF_000277125.1", "gtdb_species": "s__Mycobacterium intracellulare", "ani": 87.4419, "matched_fragments": 1428, "total_fragments": 1925, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "95.71", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 82, "status": "-" }, { "accession": "GCF_002105755.1", "gtdb_species": "s__Mycobacterium colombiense", "ani": 87.1009, "matched_fragments": 1421, "total_fragments": 1925, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_010731675.1", "gtdb_species": "s__Mycobacterium marseillense", "ani": 87.0815, "matched_fragments": 1382, "total_fragments": 1925, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001672755.1", "gtdb_species": "s__Mycobacterium colombiense_C", "ani": 86.8978, "matched_fragments": 1374, "total_fragments": 1925, "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_001665835.1", "gtdb_species": "s__Mycobacterium colombiense_A", "ani": 86.8831, "matched_fragments": 1375, "total_fragments": 1925, "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": 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1, "status": "-" }, { "accession": "GCA_004298145.1", "gtdb_species": "s__Mycobacterium sp004298145", "ani": 86.6847, "matched_fragments": 1347, "total_fragments": 1925, "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_003284975.1", "gtdb_species": "s__Mycobacterium europaeum_A", "ani": 86.6271, "matched_fragments": 1294, "total_fragments": 1925, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.84", "min_intra_species_ani": "95.70", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 6, "status": "-" }, { 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycobacterium", "timonense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }