{ "type": "genome", "identifier": "GCF_018278905.1", "organism": "Mycobacterium spongiae", "title": "Mycobacterium spongiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Melbourne", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018278905.1", "bioproject": "PRJNA224116", "biosample": "SAMN12776813", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "886343", "species_taxid": "886343", "organism_name": "Mycobacterium spongiae", "infraspecific_name": "strain=FSD4b-SM", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/05", "asm_name": "ASM1827890v1", "asm_submitter": "University of Melbourne", "gbrs_paired_asm": "GCA_018278905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/278/905/GCF_018278905.1_ASM1827890v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5581157", "genome_size_ungapped": "5581157", "gc_percent": "65.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018278905.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "4554", "protein_coding_gene_count": "4359", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-05", "dateModified": "2021-05-05", "datePublished": "2021-05-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium spongiae" ], "sample_taxid": [ "886343" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia: Off the coast near Cooktown, Great Barrier Reef, depth 25 metres" ], "sample_host_location_id": [], "data_size": "1.512 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)": "5581157", "Number of Sequences": "1", "Longest Sequences (bp)": "5581157", "N50 (bp)": "5581157", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.6", "Number of CDSs": "4610", "Average Protein Length": "360.4", "Coding Ratio (%)": "89.3", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "8" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium spongiae", "strain": "strain=FSD4b-SM", "accession": "GCA_018278905.1", "taxid": 886343, "species_taxid": 886343, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1856, "total_fragments": 1860, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium lacus", "strain": "strain=DSM 44577", "accession": "GCA_002102215.1", "taxid": 169765, "species_taxid": 169765, "relation_to_type": "type", "validated": true, "ani": 80.554, "matched_fragments": 960, "total_fragments": 1860, "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": 80.4781, "matched_fragments": 990, "total_fragments": 1860, "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": 80.3781, "matched_fragments": 926, "total_fragments": 1860, "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": 80.343, "matched_fragments": 900, "total_fragments": 1860, "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": 80.092, "matched_fragments": 850, "total_fragments": 1860, "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": 80.0886, "matched_fragments": 870, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium simulans", "strain": "strain=FI-09026", "accession": "GCA_900232995.1", "taxid": 627089, "species_taxid": 627089, "relation_to_type": "type", "validated": true, "ani": 79.8586, "matched_fragments": 967, "total_fragments": 1860, "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": 79.6949, "matched_fragments": 844, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium ostraviense", "strain": "strain=241/15", "accession": "GCA_002705925.1", "taxid": 2738409, "species_taxid": 2738409, "relation_to_type": "type", "validated": true, "ani": 79.6856, "matched_fragments": 936, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium persicum", "strain": "strain=AFPC-000227", "accession": "GCA_002086675.1", "taxid": 1487726, "species_taxid": 1487726, "relation_to_type": "type", "validated": true, "ani": 79.5208, "matched_fragments": 894, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium pseudokansasii", "strain": "strain=MK142", "accession": "GCA_900566075.1", "taxid": 2341080, "species_taxid": 2341080, "relation_to_type": "type", "validated": true, "ani": 79.3919, "matched_fragments": 933, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium avium subsp. avium", "strain": "strain=ATCC 25291", "accession": "GCA_000174035.1", "taxid": 44454, "species_taxid": 1764, "relation_to_type": "type", "validated": true, "ani": 79.3314, "matched_fragments": 751, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium avium subsp. avium", "strain": "strain=DSM 44156", "accession": "GCA_009741445.1", "taxid": 44454, "species_taxid": 1764, "relation_to_type": "type", "validated": true, "ani": 79.3217, "matched_fragments": 791, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium nebraskense", "strain": "strain=DSM 44803", "accession": "GCA_002102255.1", "taxid": 244292, "species_taxid": 244292, "relation_to_type": "type", "validated": true, "ani": 79.3002, "matched_fragments": 812, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium helveticum", "strain": "strain=16-83", "accession": "GCA_007714205.1", "taxid": 2592811, "species_taxid": 2592811, "relation_to_type": "type", "validated": true, "ani": 79.2803, "matched_fragments": 762, "total_fragments": 1860, "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": 79.221, "matched_fragments": 787, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium bohemicum", "strain": "strain=DSM 44277", "accession": "GCA_001053185.1", "taxid": 56425, "species_taxid": 56425, "relation_to_type": "type", "validated": true, "ani": 79.1748, "matched_fragments": 751, "total_fragments": 1860, "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": 79.1499, "matched_fragments": 778, "total_fragments": 1860, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018278905.1", "gtdb_species": "s__Mycobacterium spongiae", "ani": 100.0, "matched_fragments": 1856, "total_fragments": 1860, "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": "conclusive" }, { "accession": "GCF_002104675.1", "gtdb_species": "s__Mycobacterium decipiens", "ani": 80.845, "matched_fragments": 1009, "total_fragments": 1860, "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_010731535.1", "gtdb_species": "s__Mycobacterium lacus", "ani": 80.4576, "matched_fragments": 996, "total_fragments": 1860, "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": 80.3807, "matched_fragments": 925, "total_fragments": 1860, "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_002102175.1", "gtdb_species": "s__Mycobacterium gastri", "ani": 79.7768, "matched_fragments": 904, "total_fragments": 1860, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002705925.1", "gtdb_species": "s__Mycobacterium ostraviense", "ani": 79.6929, "matched_fragments": 932, "total_fragments": 1860, "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_900157385.1", "gtdb_species": "s__Mycobacterium terramassiliense", "ani": 79.692, "matched_fragments": 860, "total_fragments": 1860, "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_900566055.1", "gtdb_species": "s__Mycobacterium innocens", "ani": 79.6919, "matched_fragments": 894, "total_fragments": 1860, "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_002101815.1", "gtdb_species": "s__Mycobacterium paraense", "ani": 79.6789, "matched_fragments": 845, "total_fragments": 1860, "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": 79.6789, "matched_fragments": 818, "total_fragments": 1860, "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": 79.6024, "matched_fragments": 822, "total_fragments": 1860, "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": 79.5657, "matched_fragments": 877, "total_fragments": 1860, "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_001665295.1", "gtdb_species": "s__Mycobacterium sp001665295", "ani": 79.5459, "matched_fragments": 856, "total_fragments": 1860, "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_002086675.1", "gtdb_species": "s__Mycobacterium persicum", "ani": 79.5367, "matched_fragments": 892, "total_fragments": 1860, "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": 79.3924, "matched_fragments": 930, "total_fragments": 1860, "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_009741445.1", "gtdb_species": "s__Mycobacterium avium", "ani": 79.3253, "matched_fragments": 790, "total_fragments": 1860, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 96.9043, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.29", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 206, "status": "-" }, { "accession": "GCF_002102255.1", "gtdb_species": "s__Mycobacterium nebraskense", "ani": 79.298, "matched_fragments": 812, "total_fragments": 1860, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001667275.1", "gtdb_species": "s__Mycobacterium sp001667275", "ani": 79.2653, "matched_fragments": 768, "total_fragments": 1860, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.42", "min_intra_species_ani": "96.39", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001053185.1", "gtdb_species": "s__Mycobacterium bohemicum", "ani": 79.1879, "matched_fragments": 748, "total_fragments": 1860, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010731775.1", "gtdb_species": "s__Mycobacterium mantenii", "ani": 79.1541, "matched_fragments": 777, "total_fragments": 1860, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.19", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "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", "spongiae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }