{ "type": "genome", "identifier": "GCF_003266045.1", "organism": "Mycobacterium tuberculosis H37Rv", "title": "Mycobacterium tuberculosis H37Rv", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of British Columbia", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003266045.1", "bioproject": "PRJNA224116", "biosample": "SAMN07572166", "wgs_master": "NVQJ00000000.1", "refseq_category": "na", "taxid": "83332", "species_taxid": "1773", "organism_name": "Mycobacterium tuberculosis H37Rv", "infraspecific_name": "strain=H37Rv", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/26", "asm_name": "ASM326604v1", "asm_submitter": "University of British Columbia", "gbrs_paired_asm": "GCA_003266045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/266/045/GCF_003266045.1_ASM326604v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4356336", "genome_size_ungapped": "4356336", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "167", "contig_count": "167", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003266045.1-RS_2024_07_02", "annotation_date": "2024-07-02", "total_gene_count": "4270", "protein_coding_gene_count": "3956", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-26", "dateModified": "2018-06-26", "datePublished": "2018-06-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium tuberculosis H37Rv" ], "sample_taxid": [ "83332" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.219 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)": "4356336", "Number of Sequences": "167", "Longest Sequences (bp)": "278654", "N50 (bp)": "66497", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.5", "Number of CDSs": "3955", "Average Protein Length": "318.4", "Coding Ratio (%)": "86.7", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "7" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium tuberculosis", "strain": "strain=H37Rv", "accession": "GCA_003266045.1", "taxid": 1773, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1381, "total_fragments": 1384, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium tuberculosis", "strain": "strain=H37Rv", "accession": "GCA_000277735.2", "taxid": 1773, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 99.99, "matched_fragments": 1383, "total_fragments": 1384, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium tuberculosis", "strain": "strain=H37Rv", "accession": "GCA_000195955.2", "taxid": 1773, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 99.9888, "matched_fragments": 1383, "total_fragments": 1384, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium tuberculosis", "strain": "strain=H37Rv", "accession": "GCA_000667805.1", "taxid": 1773, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 99.9761, "matched_fragments": 1380, "total_fragments": 1384, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium tuberculosis variant africanum", "strain": "strain=ATCC 25420", "accession": "GCA_002982335.1", "taxid": 33894, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 99.8633, "matched_fragments": 1332, "total_fragments": 1384, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium tuberculosis variant microti", "strain": "strain=ATCC 19422", "accession": "GCA_002982215.1", "taxid": 1806, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 99.8086, "matched_fragments": 1239, "total_fragments": 1384, "ani_threshold": 95, "status": "conclusive" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000195955.2", "gtdb_species": "s__Mycobacterium tuberculosis", "ani": 99.9888, "matched_fragments": 1383, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.91", "num_clustered_genomes": 6836, "status": "conclusive" }, { "accession": "GCF_002104675.1", "gtdb_species": "s__Mycobacterium decipiens", "ani": 85.9944, "matched_fragments": 1105, "total_fragments": 1384, "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_010730055.1", "gtdb_species": "s__Mycobacterium shinjukuense", "ani": 83.5143, "matched_fragments": 1037, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010731535.1", "gtdb_species": "s__Mycobacterium lacus", "ani": 82.5756, "matched_fragments": 1047, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002086305.1", "gtdb_species": "s__Mycobacterium malmoense_B", "ani": 81.7648, "matched_fragments": 877, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002101845.1", "gtdb_species": "s__Mycobacterium riyadhense", "ani": 81.6743, "matched_fragments": 996, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.30", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_002705925.1", "gtdb_species": "s__Mycobacterium ostraviense", "ani": 81.2684, "matched_fragments": 971, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900566055.1", "gtdb_species": "s__Mycobacterium innocens", "ani": 81.2547, "matched_fragments": 914, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001667015.1", "gtdb_species": "s__Mycobacterium sp001667015", "ani": 81.1241, "matched_fragments": 820, "total_fragments": 1384, "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_001954195.1", "gtdb_species": "s__Mycobacterium sp001954195", "ani": 81.1055, "matched_fragments": 822, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.85", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002086675.1", "gtdb_species": "s__Mycobacterium persicum", "ani": 81.0864, "matched_fragments": 921, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.58", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_900566075.1", "gtdb_species": "s__Mycobacterium pseudokansasii", "ani": 81.0304, "matched_fragments": 949, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "99.48", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002101815.1", "gtdb_species": "s__Mycobacterium paraense", "ani": 80.9947, "matched_fragments": 847, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002086635.1", "gtdb_species": "s__Mycobacterium alsense", "ani": 80.9363, "matched_fragments": 838, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.76", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001665295.1", "gtdb_species": "s__Mycobacterium sp001665295", "ani": 80.8593, "matched_fragments": 845, "total_fragments": 1384, "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_900157385.1", "gtdb_species": "s__Mycobacterium terramassiliense", "ani": 80.843, "matched_fragments": 855, "total_fragments": 1384, "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_007714205.1", "gtdb_species": "s__Mycobacterium helveticum", "ani": 80.5788, "matched_fragments": 783, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003614435.1", "gtdb_species": "s__Mycobacterium paragordonae", "ani": 80.1096, "matched_fragments": 832, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_002101735.1", "gtdb_species": "s__Mycobacterium kyorinense", "ani": 79.8972, "matched_fragments": 673, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002101595.1", "gtdb_species": "s__Mycobacterium celatum", "ani": 79.6759, "matched_fragments": 715, "total_fragments": 1384, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001499905.1", "gtdb_species": "s__Mycobacterium sp001499905", "ani": 78.1479, "matched_fragments": 414, "total_fragments": 1384, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": 0.0, "doubling_h": 1.226, "growth_tmp": 37.333, "optimum_tmp": 36.898, "optimum_ph": 6.706, "genome_size": 4368332.551, "gc_content": 65.54, "coding_genes": 4082.958, "rRNA16S_genes": 1.0, "tRNA_genes": 44.994, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycobacterium", "tuberculosis", "H37Rv" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }