{ "type": "genome", "identifier": "GCF_025823035.1", "organism": "Mycobacterium haemophilum DSM 44634", "title": "Mycobacterium haemophilum DSM 44634", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Uppsala University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025823035.1", "bioproject": "PRJNA224116", "biosample": "SAMN15568927", "wgs_master": "JACKVB000000000.1", "refseq_category": "na", "taxid": "1202450", "species_taxid": "29311", "organism_name": "Mycobacterium haemophilum DSM 44634", "infraspecific_name": "strain=DSM 44634", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/24", "asm_name": "ASM2582303v1", "asm_submitter": "Uppsala University", "gbrs_paired_asm": "GCA_025823035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/823/035/GCF_025823035.1_ASM2582303v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4226694", "genome_size_ungapped": "4225978", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025823035.1-RS_2024_08_02", "annotation_date": "2024-08-02", "total_gene_count": "4080", "protein_coding_gene_count": "3735", "non_coding_gene_count": "51", "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 haemophilum DSM 44634" ], "sample_taxid": [ "1202450" ], "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": "1.185 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 30.0, "max": 30.0 }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4226694", "Number of Sequences": "37", "Longest Sequences (bp)": "578875", "N50 (bp)": "218562", "Gap Ratio (%)": "0.025244", "GCcontent (%)": "63.9", "Number of CDSs": "3922", "Average Protein Length": "313.7", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium haemophilum", "strain": "strain=ATCC 29548", "accession": "GCA_000340435.3", "taxid": 29311, "species_taxid": 29311, "relation_to_type": "type", "validated": true, "ani": 99.985, "matched_fragments": 1388, "total_fragments": 1391, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium lepromatosis", "strain": "strain=FJ924", "accession": "GCA_000975265.2", "taxid": 480418, "species_taxid": 480418, "relation_to_type": "type", "validated": true, "ani": 84.9403, "matched_fragments": 903, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium heidelbergense", "strain": "strain=DSM 44471", "accession": "GCA_002086215.1", "taxid": 53376, "species_taxid": 53376, "relation_to_type": "type", "validated": true, "ani": 82.1651, "matched_fragments": 884, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium heidelbergense", "strain": "strain=JCM 14842", "accession": "GCA_010730745.1", "taxid": 53376, "species_taxid": 53376, "relation_to_type": "type", "validated": true, "ani": 82.1346, "matched_fragments": 898, "total_fragments": 1391, "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": 81.9825, "matched_fragments": 930, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium lacus", "strain": "strain=JCM 15657", "accession": "GCA_010731535.1", "taxid": 169765, "species_taxid": 169765, "relation_to_type": "type", "validated": true, "ani": 81.9415, "matched_fragments": 954, "total_fragments": 1391, "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": 81.3343, "matched_fragments": 845, "total_fragments": 1391, "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": 81.2847, "matched_fragments": 866, "total_fragments": 1391, "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": 81.2001, "matched_fragments": 871, "total_fragments": 1391, "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": 81.1309, "matched_fragments": 879, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium paraense", "strain": "strain=IEC26", "accession": "GCA_002101815.1", "taxid": 767916, "species_taxid": 767916, "relation_to_type": "type", "validated": true, "ani": 81.0506, "matched_fragments": 866, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "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": 80.9153, "matched_fragments": 850, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium tuberculosis", "strain": "strain=H37Rv", "accession": "GCA_000195955.2", "taxid": 1773, "species_taxid": 1773, "relation_to_type": "type", "validated": true, "ani": 80.8974, "matched_fragments": 878, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "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": 80.8682, "matched_fragments": 805, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium riyadhense", "strain": "strain=DSM 45176", "accession": "GCA_002101845.1", "taxid": 486698, "species_taxid": 486698, "relation_to_type": "type", "validated": true, "ani": 80.8156, "matched_fragments": 901, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium innocens", "strain": "strain=MK13", "accession": "GCA_900566055.1", "taxid": 2341083, "species_taxid": 2341083, "relation_to_type": "type", "validated": true, "ani": 80.5185, "matched_fragments": 848, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium angelicum", "strain": "strain=DSM 45057", "accession": "GCA_002086155.1", "taxid": 470074, "species_taxid": 470074, "relation_to_type": "type", "validated": true, "ani": 80.4538, "matched_fragments": 843, "total_fragments": 1391, "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": 80.4218, "matched_fragments": 830, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium bohemicum", "strain": "strain=DSM 44277", "accession": "GCA_002102025.1", "taxid": 56425, "species_taxid": 56425, "relation_to_type": "type", "validated": true, "ani": 80.2882, "matched_fragments": 803, "total_fragments": 1391, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000340435.2", "gtdb_species": "s__Mycobacterium haemophilum", "ani": 99.985, "matched_fragments": 1388, "total_fragments": 1391, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_000195855.1", "gtdb_species": "s__Mycobacterium leprae", "ani": 85.2096, "matched_fragments": 913, "total_fragments": 1391, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.91", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000966355.1", "gtdb_species": "s__Mycobacterium lepromatosis", "ani": 85.1035, "matched_fragments": 870, "total_fragments": 1391, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.85", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003408705.1", "gtdb_species": "s__Mycobacterium uberis", "ani": 85.0117, "matched_fragments": 881, "total_fragments": 1391, "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_002086305.1", "gtdb_species": "s__Mycobacterium malmoense_B", "ani": 82.1743, "matched_fragments": 927, "total_fragments": 1391, "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_010730745.1", "gtdb_species": "s__Mycobacterium heidelbergense", "ani": 82.1492, "matched_fragments": 896, "total_fragments": 1391, "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_010731535.1", "gtdb_species": "s__Mycobacterium lacus", "ani": 81.9108, "matched_fragments": 957, "total_fragments": 1391, "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": 81.2776, "matched_fragments": 868, "total_fragments": 1391, "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_001667035.1", "gtdb_species": "s__Mycobacterium sp001667035", "ani": 81.2699, "matched_fragments": 883, "total_fragments": 1391, "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": 81.129, "matched_fragments": 879, "total_fragments": 1391, "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_002101815.1", "gtdb_species": "s__Mycobacterium paraense", "ani": 81.0659, "matched_fragments": 864, "total_fragments": 1391, "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_001667015.1", "gtdb_species": "s__Mycobacterium sp001667015", "ani": 80.9563, "matched_fragments": 834, "total_fragments": 1391, "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_000195955.2", "gtdb_species": "s__Mycobacterium tuberculosis", "ani": 80.8876, "matched_fragments": 879, "total_fragments": 1391, "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": "-" }, { "accession": "GCF_001667115.1", "gtdb_species": "s__Mycobacterium sp001667115", "ani": 80.7931, "matched_fragments": 822, "total_fragments": 1391, "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_002101845.1", "gtdb_species": "s__Mycobacterium riyadhense", "ani": 80.7875, "matched_fragments": 904, "total_fragments": 1391, "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_900566055.1", "gtdb_species": "s__Mycobacterium innocens", "ani": 80.5009, "matched_fragments": 851, "total_fragments": 1391, "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_002086155.1", "gtdb_species": "s__Mycobacterium angelicum", "ani": 80.4602, "matched_fragments": 841, "total_fragments": 1391, "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_008370645.1", "gtdb_species": "s__Mycobacterium simiae_A", "ani": 79.608, "matched_fragments": 714, "total_fragments": 1391, "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": -0.398, "cell_length": 0.146, "doubling_h": 1.493, "growth_tmp": 31.0, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 4290772.11, "gc_content": 63.925, "coding_genes": 3736.0, "rRNA16S_genes": 1.0, "tRNA_genes": 45.0, "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": 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", "haemophilum", "DSM", "44634" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }