{ "type": "genome", "identifier": "GCF_002086165.1", "organism": "Mycobacterium bouchedurhonense", "title": "Mycobacterium bouchedurhonense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "San Raffaele Scientific Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002086165.1", "bioproject": "PRJNA224116", "biosample": "SAMN06064234", "wgs_master": "MVHL00000000.1", "refseq_category": "reference genome", "taxid": "701041", "species_taxid": "701041", "organism_name": "Mycobacterium bouchedurhonense", "infraspecific_name": "strain=DSM 45439", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/11", "asm_name": "ASM208616v1", "asm_submitter": "San Raffaele Scientific Institute", "gbrs_paired_asm": "GCA_002086165.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/086/165/GCF_002086165.1_ASM208616v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5897311", "genome_size_ungapped": "5897311", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "230", "contig_count": "230", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002086165.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "5768", "protein_coding_gene_count": "5477", "non_coding_gene_count": "83", "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 bouchedurhonense" ], "sample_taxid": [ "701041" ], "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": "1.619 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)": "5897311", "Number of Sequences": "230", "Longest Sequences (bp)": "333945", "N50 (bp)": "95182", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.6", "Number of CDSs": "5634", "Average Protein Length": "307.3", "Coding Ratio (%)": "88.1", "Number of rRNAs": "3", "Number of tRNAs": "85", "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": 98.8356, "matched_fragments": 1494, "total_fragments": 1865, "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": 98.7446, "matched_fragments": 1382, "total_fragments": 1865, "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": 87.446, "matched_fragments": 1412, "total_fragments": 1865, "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": 87.4312, "matched_fragments": 1413, "total_fragments": 1865, "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": 87.3542, "matched_fragments": 1397, "total_fragments": 1865, "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": 87.3393, "matched_fragments": 1242, "total_fragments": 1865, "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": 87.2945, "matched_fragments": 1410, "total_fragments": 1865, "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": 87.2929, "matched_fragments": 1392, "total_fragments": 1865, "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": 87.1573, "matched_fragments": 1354, "total_fragments": 1865, "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": 87.1258, "matched_fragments": 1394, "total_fragments": 1865, "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": 87.0704, "matched_fragments": 1341, "total_fragments": 1865, "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": 87.0597, "matched_fragments": 1404, "total_fragments": 1865, "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": 86.5896, "matched_fragments": 1430, "total_fragments": 1865, "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": 86.1905, "matched_fragments": 1297, "total_fragments": 1865, "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": 83.6761, "matched_fragments": 1214, "total_fragments": 1865, "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": 83.1475, "matched_fragments": 1077, "total_fragments": 1865, "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": 82.2206, "matched_fragments": 998, "total_fragments": 1865, "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": 80.9944, "matched_fragments": 943, "total_fragments": 1865, "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": 80.9571, "matched_fragments": 948, "total_fragments": 1865, "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": 80.5824, "matched_fragments": 897, "total_fragments": 1865, "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": 80.5814, "matched_fragments": 883, "total_fragments": 1865, "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": 80.4571, "matched_fragments": 898, "total_fragments": 1865, "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": 80.3528, "matched_fragments": 835, "total_fragments": 1865, "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": 80.3454, "matched_fragments": 823, "total_fragments": 1865, "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": 80.2076, "matched_fragments": 782, "total_fragments": 1865, "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": 80.1439, "matched_fragments": 792, "total_fragments": 1865, "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": 79.9421, "matched_fragments": 754, "total_fragments": 1865, "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": 79.3792, "matched_fragments": 755, "total_fragments": 1865, "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": 79.3524, "matched_fragments": 812, "total_fragments": 1865, "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": 79.3104, "matched_fragments": 754, "total_fragments": 1865, "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": 98.8454, "matched_fragments": 1493, "total_fragments": 1865, "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": "conclusive" }, { "accession": "GCA_002291465.1", "gtdb_species": "s__Mycobacterium lepraemurium", "ani": 96.8818, "matched_fragments": 1278, "total_fragments": 1865, "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": "-" }, { "accession": "GCF_000277125.1", "gtdb_species": "s__Mycobacterium intracellulare", "ani": 87.4235, "matched_fragments": 1414, "total_fragments": 1865, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", 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"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_001672755.1", "gtdb_species": "s__Mycobacterium colombiense_C", "ani": 86.9008, "matched_fragments": 1346, "total_fragments": 1865, "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_003284935.1", "gtdb_species": "s__Mycobacterium arosiense_A", "ani": 86.8839, "matched_fragments": 1298, "total_fragments": 1865, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", 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"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_001667145.1", "gtdb_species": "s__Mycobacterium sp001667145", "ani": 85.6996, "matched_fragments": 1294, "total_fragments": 1865, "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_002086735.1", "gtdb_species": "s__Mycobacterium scrofulaceum", "ani": 84.6797, "matched_fragments": 1309, "total_fragments": 1865, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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