{ "type": "genome", "identifier": "GCF_002086775.1", "organism": "Mycobacterium timonense", "title": "Mycobacterium timonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "San Raffaele Scientific Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002086775.1", "bioproject": "PRJNA224116", "biosample": "SAMN06064261", "wgs_master": "MVIL00000000.1", "refseq_category": "na", "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": "2017/04/11", "asm_name": "ASM208677v1", "asm_submitter": "San Raffaele Scientific Institute", "gbrs_paired_asm": "GCA_002086775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/086/775/GCF_002086775.1_ASM208677v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6009989", "genome_size_ungapped": "6009989", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "1217", "contig_count": "1217", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002086775.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "6402", "protein_coding_gene_count": "5787", "non_coding_gene_count": "76", "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": [ "Mycobacterium timonense" ], "sample_taxid": [ "701043" ], "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": "1.679 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)": "6009989", "Number of Sequences": "1217", "Longest Sequences (bp)": "170498", "N50 (bp)": "37351", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.5", "Number of CDSs": "5261", "Average Protein Length": "301.8", "Coding Ratio (%)": "79.3", "Number of rRNAs": "2", "Number of tRNAs": "79", "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": 98.8261, "matched_fragments": 1460, "total_fragments": 1654, "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": 98.7138, "matched_fragments": 1359, "total_fragments": 1654, "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": 87.4446, "matched_fragments": 1376, "total_fragments": 1654, "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": 87.4416, "matched_fragments": 1375, "total_fragments": 1654, "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": 87.353, "matched_fragments": 1337, "total_fragments": 1654, "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": 87.3178, "matched_fragments": 1383, "total_fragments": 1654, "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": 87.2993, "matched_fragments": 1385, "total_fragments": 1654, "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": 87.2779, "matched_fragments": 1245, "total_fragments": 1654, "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": 87.0368, "matched_fragments": 1334, "total_fragments": 1654, "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": 86.9821, "matched_fragments": 1328, "total_fragments": 1654, "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": 86.98, "matched_fragments": 1377, "total_fragments": 1654, "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": 86.9703, "matched_fragments": 1372, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium mantenii", "strain": "strain=DSM 45255", "accession": "GCA_002086335.1", "taxid": 560555, "species_taxid": 560555, "relation_to_type": "type", "validated": true, "ani": 86.5788, "matched_fragments": 1364, "total_fragments": 1654, "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": 86.5669, "matched_fragments": 1389, "total_fragments": 1654, "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": 86.2257, "matched_fragments": 1269, "total_fragments": 1654, "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": 83.6416, "matched_fragments": 1212, "total_fragments": 1654, "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": 80.8514, "matched_fragments": 935, "total_fragments": 1654, "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": 80.6262, "matched_fragments": 890, "total_fragments": 1654, "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": 80.6137, "matched_fragments": 868, "total_fragments": 1654, "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": 80.5415, "matched_fragments": 881, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fallax", "strain": "strain=DSM 44179", "accession": "GCA_002101995.1", "taxid": 1793, "species_taxid": 1793, "relation_to_type": "type", "validated": true, "ani": 80.4131, "matched_fragments": 740, "total_fragments": 1654, "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": 80.3932, "matched_fragments": 846, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium fallax", "strain": "strain=JCM 6405", "accession": "GCA_010726955.1", "taxid": 1793, "species_taxid": 1793, "relation_to_type": "type", "validated": true, "ani": 80.3799, "matched_fragments": 751, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium chitae", "strain": "strain=JCM 12403", "accession": "GCA_010727725.1", "taxid": 1792, "species_taxid": 1792, "relation_to_type": "type", "validated": true, "ani": 80.1713, "matched_fragments": 809, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium neworleansense", "strain": "strain=type strain: ATCC 49404", "accession": "GCA_001245615.1", "taxid": 146018, "species_taxid": 146018, "relation_to_type": "type", "validated": true, "ani": 79.583, "matched_fragments": 765, "total_fragments": 1654, "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": 79.3368, "matched_fragments": 772, "total_fragments": 1654, "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": 98.807, "matched_fragments": 1462, "total_fragments": 1654, "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": 96.9338, "matched_fragments": 1242, "total_fragments": 1654, "gtdb_taxonomy": 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