{ "type": "genome", "identifier": "GCF_002245535.1", "organism": "Mycobacterium lehmannii", "title": "Mycobacterium lehmannii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northumbria University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002245535.1", "bioproject": "PRJNA224116", "biosample": "SAMN07269029", "wgs_master": "NKCN00000000.1", "refseq_category": "na", "taxid": "2048550", "species_taxid": "2048550", "organism_name": "Mycobacterium lehmannii", "infraspecific_name": "strain=CECT 8763", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/08/10", "asm_name": "ASM224553v1", "asm_submitter": "Northumbria University", "gbrs_paired_asm": "GCA_002245535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/245/535/GCF_002245535.1_ASM224553v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5496052", "genome_size_ungapped": "5496052", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "76", "contig_count": "76", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-20", "total_gene_count": "5407", "protein_coding_gene_count": "5240", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-08-10", "dateModified": "2017-08-10", "datePublished": "2017-08-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium lehmannii" ], "sample_taxid": [ "2048550" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.514 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)": "5496052", "Number of Sequences": "76", "Longest Sequences (bp)": "467790", "N50 (bp)": "178807", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.7", "Number of CDSs": "5318", "Average Protein Length": "315.8", "Coding Ratio (%)": "91.7", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium lehmannii", "strain": "strain=CECT 8763", "accession": "GCA_002245535.1", "taxid": 2048550, "species_taxid": 2048550, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1792, "total_fragments": 1793, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycobacterium neumannii", "strain": "strain=CECT 8766", "accession": "GCA_002245615.1", "taxid": 2048551, "species_taxid": 2048551, "relation_to_type": "type", "validated": true, "ani": 95.195, "matched_fragments": 1484, "total_fragments": 1793, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacterium malmesburyense", "strain": "strain=WCM 7299", "accession": "GCA_001050015.1", "taxid": 1566886, "species_taxid": 1566886, "relation_to_type": "type", "validated": true, "ani": 87.6435, "matched_fragments": 1377, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium komanii", "strain": "strain=GPK 1020", "accession": "GCA_001050035.1", "taxid": 1566885, "species_taxid": 1566885, "relation_to_type": "type", "validated": true, "ani": 87.5092, "matched_fragments": 1391, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium celeriflavum", "strain": "strain=DSM 46765", "accession": "GCA_002086175.1", "taxid": 1249101, "species_taxid": 1249101, "relation_to_type": "type", "validated": true, "ani": 84.4824, "matched_fragments": 1240, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium rutilum", "strain": "strain=DSM 45405", "accession": "GCA_900108565.1", "taxid": 370526, "species_taxid": 370526, "relation_to_type": "type", "validated": true, "ani": 84.3113, "matched_fragments": 1310, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium phlei", "strain": "strain=DSM 43239 = CCUG 21000", "accession": "GCA_001582015.1", "taxid": 1771, "species_taxid": 1771, "relation_to_type": "type", "validated": true, "ani": 82.8207, "matched_fragments": 1159, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium moriokaense", "strain": "strain=CIP105393", "accession": "GCA_002086395.1", "taxid": 39691, "species_taxid": 39691, "relation_to_type": "type", "validated": true, "ani": 80.9925, "matched_fragments": 1055, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium gadium", "strain": "strain=JCM 12688", "accession": "GCA_010728925.1", "taxid": 1794, "species_taxid": 1794, "relation_to_type": "type", "validated": true, "ani": 80.8526, "matched_fragments": 1076, "total_fragments": 1793, "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": 80.1802, "matched_fragments": 855, "total_fragments": 1793, "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": 80.1631, "matched_fragments": 848, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium thermoresistibile", "strain": "strain=JCM6362", "accession": "GCA_001570505.1", "taxid": 1797, "species_taxid": 1797, "relation_to_type": "type", "validated": true, "ani": 80.1414, "matched_fragments": 858, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium arabiense", "strain": "strain=JCM 18538", "accession": "GCA_010731815.2", "taxid": 1286181, "species_taxid": 1286181, "relation_to_type": "type", "validated": true, "ani": 79.8283, "matched_fragments": 879, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium crocinum", "strain": "strain=JCM 16369", "accession": "GCA_022370635.3", "taxid": 388459, "species_taxid": 388459, "relation_to_type": "type", "validated": true, "ani": 79.7617, "matched_fragments": 859, "total_fragments": 1793, "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": 79.5727, "matched_fragments": 718, "total_fragments": 1793, "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": 79.4656, "matched_fragments": 782, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium mengxianglii", "strain": "strain=Z-34", "accession": "GCA_015710575.2", "taxid": 2736649, "species_taxid": 2736649, "relation_to_type": "type", "validated": true, "ani": 78.9662, "matched_fragments": 713, "total_fragments": 1793, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002245535.1", "gtdb_species": "s__Mycobacterium lehmannii", "ani": 100.0, "matched_fragments": 1792, "total_fragments": 1793, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.2034, "mean_intra_species_ani": "97.95", "min_intra_species_ani": "97.72", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "inconclusive" }, { "accession": "GCA_900637135.1", "gtdb_species": "s__Mycobacterium flavescens", "ani": 95.2073, "matched_fragments": 1500, "total_fragments": 1793, 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