{ "type": "genome", "identifier": "GCF_002101585.1", "organism": "Mycolicibacter engbaekii", "title": "Mycolicibacter engbaekii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Trento", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002101585.1", "bioproject": "PRJNA224116", "biosample": "SAMN04216923", "wgs_master": "LQOT00000000.1", "refseq_category": "reference genome", "taxid": "188915", "species_taxid": "188915", "organism_name": "Mycolicibacter engbaekii", "infraspecific_name": "strain=ATCC 27353", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/20", "asm_name": "ASM210158v1", "asm_submitter": "University of Trento", "gbrs_paired_asm": "GCA_002101585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/101/585/GCF_002101585.1_ASM210158v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4521435", "genome_size_ungapped": "4521435", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "79", "contig_count": "79", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-11", "total_gene_count": "4200", "protein_coding_gene_count": "4073", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-20", "dateModified": "2017-04-20", "datePublished": "2017-04-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycolicibacter engbaekii" ], "sample_taxid": [ "188915" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Denmark: Copenhagen" ], "sample_host_location_id": [], "data_size": "1.235 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)": "4521435", "Number of Sequences": "79", "Longest Sequences (bp)": "355874", "N50 (bp)": "132590", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.5", "Number of CDSs": "4132", "Average Protein Length": "334.6", "Coding Ratio (%)": "91.7", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycolicibacter engbaekii", "strain": "strain=ATCC 27353", "accession": "GCA_002101585.1", "taxid": 188915, "species_taxid": 188915, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1459, "total_fragments": 1463, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacter hiberniae", "strain": "strain=JCM 13571", "accession": "GCA_010729485.1", "taxid": 29314, "species_taxid": 29314, "relation_to_type": "type", "validated": true, "ani": 95.3331, "matched_fragments": 1322, "total_fragments": 1463, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacter hiberniae", "strain": "strain=ATCC 49874", "accession": "GCA_002101655.1", "taxid": 29314, "species_taxid": 29314, "relation_to_type": "type", "validated": true, "ani": 95.329, "matched_fragments": 1309, "total_fragments": 1463, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Mycolicibacter nonchromogenicus", "strain": "strain=DSM 44164", "accession": "GCA_002101775.1", "taxid": 1782, "species_taxid": 1782, "relation_to_type": "type", "validated": true, "ani": 86.2188, "matched_fragments": 1200, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter longobardus", "strain": "strain=DSM 45394", "accession": "GCA_002102265.1", "taxid": 1108812, "species_taxid": 1108812, "relation_to_type": "type", "validated": true, "ani": 85.2949, "matched_fragments": 1129, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter minnesotensis", "strain": "strain=DSM 45633", "accession": "GCA_002086405.1", "taxid": 1118379, "species_taxid": 1118379, "relation_to_type": "type", "validated": true, "ani": 84.6814, "matched_fragments": 1071, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter minnesotensis", "strain": "strain=JCM 17932", "accession": "GCA_010731755.1", "taxid": 1118379, "species_taxid": 1118379, "relation_to_type": "type", "validated": true, "ani": 84.5864, "matched_fragments": 1098, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=CST 7247", "accession": "GCA_010093495.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 84.2976, "matched_fragments": 1049, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=DSM 45093", "accession": "GCA_002086285.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 84.2612, "matched_fragments": 1097, "total_fragments": 1463, "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": 79.3427, "matched_fragments": 700, "total_fragments": 1463, "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": 79.3056, "matched_fragments": 713, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002101585.1", "gtdb_species": "s__Mycobacterium engbaekii", "ani": 100.0, "matched_fragments": 1459, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.4017, "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": "conclusive" }, { "accession": "GCF_010729485.1", "gtdb_species": "s__Mycobacterium hiberniae", "ani": 95.3065, "matched_fragments": 1324, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.4017, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "95.62", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001021505.1", "gtdb_species": "s__Mycobacterium heraklionense_B", "ani": 86.7441, "matched_fragments": 1194, "total_fragments": 1463, "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_001673105.1", "gtdb_species": "s__Mycobacterium heraklionense_A", "ani": 86.396, "matched_fragments": 1178, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.02", "min_intra_species_ani": "95.09", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_002101775.1", "gtdb_species": "s__Mycobacterium nonchromogenicum", "ani": 86.2195, "matched_fragments": 1201, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.25", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000455125.1", "gtdb_species": "s__Mycobacterium sp000455125", "ani": 86.1699, "matched_fragments": 1181, 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null, "spiral_cell_shape": null }, "_genome_taxon": [ "Mycolicibacter", "engbaekii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }