{ "type": "genome", "identifier": "GCF_002245615.1", "organism": "Mycobacterium neumannii", "title": "Mycobacterium neumannii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northumbria University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002245615.1", "bioproject": "PRJNA224116", "biosample": "SAMN07269033", "wgs_master": "NKCO00000000.1", "refseq_category": "reference genome", "taxid": "2048551", "species_taxid": "2048551", "organism_name": "Mycobacterium neumannii", "infraspecific_name": "strain=CECT 8766", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/08/10", "asm_name": "ASM224561v1", "asm_submitter": "Northumbria University", "gbrs_paired_asm": "GCA_002245615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/245/615/GCF_002245615.1_ASM224561v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5376391", "genome_size_ungapped": "5376327", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002245615.1-RS_2024_03_27", "annotation_date": "2024-03-27", "total_gene_count": "5165", "protein_coding_gene_count": "5037", "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 neumannii" ], "sample_taxid": [ "2048551" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Unknown" ], "sample_host_location_id": [], "data_size": "1.480 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)": "5376391", "Number of Sequences": "58", "Longest Sequences (bp)": "507384", "N50 (bp)": "200051", "Gap Ratio (%)": "0.001190", "GCcontent (%)": "66.8", "Number of CDSs": "5113", "Average Protein Length": "321.0", "Coding Ratio (%)": "91.6", "Number of rRNAs": "5", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium neumannii", "strain": "strain=CECT 8766", "accession": "GCA_002245615.1", "taxid": 2048551, "species_taxid": 2048551, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1762, "total_fragments": 1766, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycobacterium lehmannii", "strain": "strain=CECT 8763", "accession": "GCA_002245535.1", "taxid": 2048550, "species_taxid": 2048550, "relation_to_type": "type", "validated": true, "ani": 95.1851, "matched_fragments": 1475, "total_fragments": 1766, "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": 87.6695, "matched_fragments": 1416, "total_fragments": 1766, "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": 87.5278, "matched_fragments": 1428, "total_fragments": 1766, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacterium celeriflavum", "strain": "strain=JCM 18439", "accession": "GCA_010731795.1", "taxid": 1249101, "species_taxid": 1249101, "relation_to_type": "type", "validated": true, "ani": 84.5033, "matched_fragments": 1289, "total_fragments": 1766, "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": 84.3993, "matched_fragments": 1282, "total_fragments": 1766, "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": 84.0395, "matched_fragments": 1281, "total_fragments": 1766, "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": 82.93, "matched_fragments": 1149, "total_fragments": 1766, "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": 80.1166, "matched_fragments": 840, "total_fragments": 1766, "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": 80.0776, "matched_fragments": 842, "total_fragments": 1766, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium pallens", "strain": "strain=JCM 16370", "accession": "GCA_019456675.1", "taxid": 370524, "species_taxid": 370524, "relation_to_type": "type", "validated": true, "ani": 79.6579, "matched_fragments": 806, "total_fragments": 1766, "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": 79.5123, "matched_fragments": 818, "total_fragments": 1766, "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": 79.4664, "matched_fragments": 735, "total_fragments": 1766, "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": 79.4432, "matched_fragments": 781, "total_fragments": 1766, "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": 79.433, "matched_fragments": 833, "total_fragments": 1766, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_900637135.1", "gtdb_species": "s__Mycobacterium flavescens", "ani": 99.9976, "matched_fragments": 1766, "total_fragments": 1766, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.2034, 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"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": 34.928, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 5658460.823, "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", "neumannii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }