{ "type": "genome", "identifier": "GCF_025822885.1", "organism": "Mycobacterium shimoidei", "title": "Mycobacterium shimoidei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025822885.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568941", "wgs_master": "JACKUN000000000.1", "refseq_category": "na", "taxid": "29313", "species_taxid": "29313", "organism_name": "Mycobacterium shimoidei", "infraspecific_name": "strain=DSM 44152", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582288v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025822885.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/822/885/GCF_025822885.1_ASM2582288v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4720881", "genome_size_ungapped": "4720642", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "46", "contig_count": "46", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025822885.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "4565", "protein_coding_gene_count": "4405", "non_coding_gene_count": "56", "pubmed_id": "36243697" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-10-24", "dateModified": "2022-10-24", "datePublished": "2022-10-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium shimoidei" ], "sample_taxid": [ "29313" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not collected" ], "sample_host_location_id": [], "data_size": "1.308 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 37.0, "max": 37.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4720881", "Number of Sequences": "46", "Longest Sequences (bp)": "534063", "N50 (bp)": "228545", "Gap Ratio (%)": "0.005973", "GCcontent (%)": "65.8", "Number of CDSs": "4498", "Average Protein Length": "323.0", "Coding Ratio (%)": "92.3", "Number of rRNAs": "4", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium kyorinense", "strain": "strain=DSM 45166", "accession": "GCA_002101735.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 82.8867, "matched_fragments": 1052, "total_fragments": 1551, "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": 82.8201, "matched_fragments": 1038, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium celatum", "strain": "strain=DSM 44243", "accession": "GCA_002101595.1", "taxid": 28045, "species_taxid": 28045, "relation_to_type": "type", "validated": true, "ani": 82.7826, "matched_fragments": 1051, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium branderi", "strain": "strain=JCM 12687", "accession": "GCA_010728725.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 82.7534, "matched_fragments": 1083, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium branderi", "strain": "strain=DSM 44624", "accession": "GCA_002086575.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 82.7238, "matched_fragments": 1060, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium celatum", "strain": "strain=ATCC 51131", "accession": "GCA_000974705.1", "taxid": 28045, "species_taxid": 28045, "relation_to_type": "type", "validated": true, "ani": 82.6771, "matched_fragments": 799, "total_fragments": 1551, "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": 81.5636, "matched_fragments": 995, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium conspicuum", "strain": "strain=DSM 44136", "accession": "GCA_002102095.1", "taxid": 44010, "species_taxid": 44010, "relation_to_type": "type", "validated": true, "ani": 80.2619, "matched_fragments": 846, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium conspicuum", "strain": "strain=JCM 14738", "accession": "GCA_010730195.1", "taxid": 44010, "species_taxid": 44010, "relation_to_type": "type", "validated": true, "ani": 80.2419, "matched_fragments": 860, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium triplex", "strain": "strain=DSM 44626", "accession": "GCA_002102415.1", "taxid": 47839, "species_taxid": 47839, "relation_to_type": "type", "validated": true, "ani": 80.1251, "matched_fragments": 821, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium triplex", "strain": "strain=DSM 44626", "accession": "GCA_000689255.1", "taxid": 47839, "species_taxid": 47839, "relation_to_type": "type", "validated": true, "ani": 80.0949, "matched_fragments": 851, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium lacus", "strain": "strain=DSM 44577", "accession": "GCA_002102215.1", "taxid": 169765, "species_taxid": 169765, "relation_to_type": "type", "validated": true, "ani": 80.0685, "matched_fragments": 769, "total_fragments": 1551, "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": 80.0651, "matched_fragments": 859, "total_fragments": 1551, "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": 80.0148, "matched_fragments": 834, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium shinjukuense", "strain": "strain=JCM 14233", "accession": "GCA_010730055.1", "taxid": 398694, "species_taxid": 398694, "relation_to_type": "type", "validated": true, "ani": 79.9566, "matched_fragments": 704, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium shinjukuense", "strain": "strain=CCUG 53584", "accession": "GCA_002086755.1", "taxid": 398694, "species_taxid": 398694, "relation_to_type": "type", "validated": true, "ani": 79.9256, "matched_fragments": 686, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter terrae", "strain": "strain=JCM 12143", "accession": "GCA_010727125.1", "taxid": 1788, "species_taxid": 1788, "relation_to_type": "type", "validated": true, "ani": 79.2327, "matched_fragments": 731, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter terrae", "strain": "strain=CIP 104321", "accession": "GCA_002101955.1", "taxid": 1788, "species_taxid": 1788, "relation_to_type": "type", "validated": true, "ani": 79.177, "matched_fragments": 728, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter hiberniae", "strain": "strain=ATCC 49874", "accession": "GCA_002101655.1", "taxid": 29314, "species_taxid": 29314, "relation_to_type": "type", "validated": true, "ani": 78.8817, "matched_fragments": 648, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002101905.1", "gtdb_species": "s__Mycobacterium shimoidei", "ani": 99.9825, "matched_fragments": 1517, "total_fragments": 1551, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.46", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_002101735.1", "gtdb_species": "s__Mycobacterium kyorinense", "ani": 82.8927, "matched_fragments": 1052, "total_fragments": 1551, "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_003402475.1", "gtdb_species": "s__Mycobacterium sp003402475", "ani": 82.8728, "matched_fragments": 1073, "total_fragments": 1551, "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_002101595.1", "gtdb_species": "s__Mycobacterium celatum", "ani": 82.782, "matched_fragments": 1050, "total_fragments": 1551, "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_010728725.1", "gtdb_species": "s__Mycobacterium branderi", "ani": 82.7607, "matched_fragments": 1082, "total_fragments": 1551, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002102185.1", "gtdb_species": "s__Mycobacterium fragae", "ani": 81.5675, "matched_fragments": 994, "total_fragments": 1551, "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": "GCA_002102225.1", "gtdb_species": "s__Mycobacterium interjectum_B", "ani": 80.3119, "matched_fragments": 895, "total_fragments": 1551, "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_900078675.2", "gtdb_species": "s__Mycobacterium interjectum", "ani": 80.3021, "matched_fragments": 861, "total_fragments": 1551, "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": "GCA_019236925.1", "gtdb_species": "s__Mycobacterium sp019236925", "ani": 80.2651, "matched_fragments": 784, "total_fragments": 1551, "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_010730195.1", "gtdb_species": "s__Mycobacterium conspicuum", "ani": 80.2298, "matched_fragments": 861, "total_fragments": 1551, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010731675.1", "gtdb_species": "s__Mycobacterium marseillense", "ani": 80.0695, "matched_fragments": 858, "total_fragments": 1551, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_010731535.1", "gtdb_species": "s__Mycobacterium lacus", "ani": 79.9815, "matched_fragments": 796, "total_fragments": 1551, "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_010730055.1", "gtdb_species": "s__Mycobacterium shinjukuense", "ani": 79.9646, "matched_fragments": 704, "total_fragments": 1551, "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_002086455.1", "gtdb_species": "s__Mycobacterium algericum", "ani": 79.4139, "matched_fragments": 701, "total_fragments": 1551, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.117, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 37.0, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 4720740.0, "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", "shimoidei" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }