{ "type": "genome", "identifier": "GCF_030812975.1", "organism": "Cytobacillus kochii", "title": "Cytobacillus kochii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030812975.1", "bioproject": "PRJNA224116", "biosample": "SAMN18243352", "wgs_master": "JAUSTS000000000.1", "refseq_category": "na", "taxid": "859143", "species_taxid": "859143", "organism_name": "Cytobacillus kochii", "infraspecific_name": "strain=DSM 23667", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/08/18", "asm_name": "ASM3081297v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_030812975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/812/975/GCF_030812975.1_ASM3081297v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4692613", "genome_size_ungapped": "4692613", "gc_percent": "36.500000", "replicon_count": "0", "scaffold_count": "44", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030812975.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "4746", "protein_coding_gene_count": "4596", "non_coding_gene_count": "104", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-08-18", "dateModified": "2023-08-18", "datePublished": "2023-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Cytobacillus kochii" ], "sample_taxid": [ "859143" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.326 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)": "4692613", "Number of Sequences": "44", "Longest Sequences (bp)": "967835", "N50 (bp)": "204395", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "36.7", "Number of CDSs": "4648", "Average Protein Length": "283.3", "Coding Ratio (%)": "84.2", "Number of rRNAs": "2", "Number of tRNAs": "89", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Cytobacillus stercorigallinarum", "strain": "strain=Sa5YUA1", "accession": "GCA_014836495.1", "taxid": 2762240, "species_taxid": 2762240, "relation_to_type": "type", "validated": true, "ani": 92.4699, "matched_fragments": 1295, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cytobacillus horneckiae", "strain": "strain=1P01SC", "accession": "GCA_002835735.1", "taxid": 549687, "species_taxid": 549687, "relation_to_type": "type", "validated": true, "ani": 78.6024, "matched_fragments": 410, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cytobacillus solani", "strain": "strain=FJAT-18043", "accession": "GCA_001420595.1", "taxid": 1637975, "species_taxid": 1637975, "relation_to_type": "type", "validated": true, "ani": 77.712, "matched_fragments": 164, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cytobacillus eiseniae", "strain": "strain=DSM 26675", "accession": "GCA_017874625.1", "taxid": 762947, "species_taxid": 762947, "relation_to_type": "type", "validated": true, "ani": 77.6877, "matched_fragments": 155, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus benzoevorans", "strain": "strain=DSM 5391", "accession": "GCA_014207535.1", "taxid": 1456, "species_taxid": 1456, "relation_to_type": "type", "validated": true, "ani": 77.6111, "matched_fragments": 78, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niallia circulans", "strain": "strain=NBRC 13626", "accession": "GCA_001591585.1", "taxid": 1397, "species_taxid": 1397, "relation_to_type": "suspected-type", "validated": true, "ani": 77.3481, "matched_fragments": 125, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neobacillus vireti", "strain": "strain=DSM 15602", "accession": "GCA_001026695.1", "taxid": 220686, "species_taxid": 220686, "relation_to_type": "type", "validated": true, "ani": 77.3471, "matched_fragments": 88, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus tepidiphilus", "strain": "strain=SYSU G01002", "accession": "GCA_009466385.1", "taxid": 2652445, "species_taxid": 2652445, "relation_to_type": "type", "validated": true, "ani": 77.2314, "matched_fragments": 77, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litchfieldia salsa", "strain": "strain=IBRC-M10078", "accession": "GCA_900104555.1", "taxid": 930152, "species_taxid": 930152, "relation_to_type": "type", "validated": true, "ani": 77.0642, "matched_fragments": 87, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neobacillus kokaensis", "strain": "strain=LOB 377", "accession": "GCA_014656545.1", "taxid": 2759023, "species_taxid": 2759023, "relation_to_type": "type", "validated": true, "ani": 77.0485, "matched_fragments": 92, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Metabacillus endolithicus", "strain": "strain=KCTC 33579", "accession": "GCA_023078335.1", "taxid": 1535204, "species_taxid": 1535204, "relation_to_type": "type", "validated": true, "ani": 77.037, "matched_fragments": 101, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neobacillus vireti", "strain": "strain=LMG 21834", "accession": "GCA_000508325.2", "taxid": 220686, "species_taxid": 220686, "relation_to_type": "type", "validated": true, "ani": 76.9131, "matched_fragments": 80, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus gaemokensis", "strain": "strain=JCM 15801", "accession": "GCA_000712615.1", "taxid": 574375, "species_taxid": 574375, "relation_to_type": "type", "validated": true, "ani": 76.8092, "matched_fragments": 98, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus gaemokensis", "strain": "strain=KCTC 13318", "accession": "GCA_001590835.1", "taxid": 574375, "species_taxid": 574375, "relation_to_type": "type", "validated": true, "ani": 76.7769, "matched_fragments": 99, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Peribacillus asahii", "strain": "strain=MA001", "accession": "GCA_003570725.1", "taxid": 228899, "species_taxid": 228899, "relation_to_type": "suspected-type", "validated": true, "ani": 76.6975, "matched_fragments": 120, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus solimangrovi", "strain": "strain=GH2-4", "accession": "GCA_001742425.1", "taxid": 1305675, "species_taxid": 1305675, "relation_to_type": "type", "validated": true, "ani": 76.4036, "matched_fragments": 68, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus tequilensis", "strain": "strain=NCTC13306", "accession": "GCA_900445435.1", "taxid": 227866, "species_taxid": 227866, "relation_to_type": "type", "validated": true, "ani": 76.3365, "matched_fragments": 52, "total_fragments": 1544, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002276165.1", "gtdb_species": "s__Cytobacillus kochii", "ani": 99.1966, "matched_fragments": 1459, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_014836495.1", "gtdb_species": "s__Cytobacillus sp014836495", "ani": 92.4699, "matched_fragments": 1295, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_002835735.1", "gtdb_species": "s__Cytobacillus horneckiae", "ani": 78.6126, "matched_fragments": 409, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005116465.1", "gtdb_species": "s__Robertmurraya kyonggiensis", "ani": 78.2113, "matched_fragments": 134, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya", "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_009849585.1", "gtdb_species": "s__Cytobacillus sp009849585", "ani": 78.178, "matched_fragments": 139, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_001956215.1", "gtdb_species": "s__Cytobacillus sp001956215", "ani": 77.8942, "matched_fragments": 130, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_001636345.1", "gtdb_species": "s__Cytobacillus gottheilii", "ani": 77.8717, "matched_fragments": 165, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.50", "min_intra_species_ani": "95.11", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900166665.1", "gtdb_species": "s__Cytobacillus gottheilii_A", "ani": 77.8395, "matched_fragments": 157, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_001420595.1", "gtdb_species": "s__Cytobacillus solani", "ani": 77.712, "matched_fragments": 164, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "99.49", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018343665.1", "gtdb_species": "s__Cytobacillus sp018343665", "ani": 77.6178, "matched_fragments": 155, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_001439605.1", "gtdb_species": "s__Cytobacillus praedii", "ani": 77.548, "matched_fragments": 174, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002860285.1", "gtdb_species": "s__Peribacillus_A sp002860285", "ani": 77.452, "matched_fragments": 74, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_A", "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_001076885.1", "gtdb_species": "s__Niallia sp001076885", "ani": 77.258, "matched_fragments": 123, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_009466385.1", "gtdb_species": "s__Bacillus_BN tepidiphilus", "ani": 77.2314, "matched_fragments": 77, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_BN", "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_002019645.1", "gtdb_species": "s__Litchfieldia alkalitelluris", "ani": 77.1721, "matched_fragments": 79, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia", "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_014656545.1", "gtdb_species": "s__Neobacillus sp014656545", "ani": 76.9946, "matched_fragments": 91, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus", "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_014837155.1", "gtdb_species": "s__Litchfieldia sp014837155", "ani": 76.9537, "matched_fragments": 105, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Litchfieldia", "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_000380245.2", "gtdb_species": "s__Bacillus_AD massiliogorillae", "ani": 76.9008, "matched_fragments": 115, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD", "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_002577655.1", "gtdb_species": "s__Metabacillus sp002577655", "ani": 76.8037, "matched_fragments": 114, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus", "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_001590835.1", "gtdb_species": "s__Bacillus_A gaemokensis", "ani": 76.801, "matched_fragments": 98, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A", "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_002561295.1", "gtdb_species": "s__Bacillus_A cereus_S", "ani": 76.4557, "matched_fragments": 101, "total_fragments": 1544, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "96.34", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Cytobacillus", "kochii" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }