{ "type": "genome", "identifier": "GCF_003201975.1", "organism": "Pseudogracilibacillus auburnensis", "title": "Pseudogracilibacillus auburnensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003201975.1", "bioproject": "PRJNA224116", "biosample": "SAMN09074764", "wgs_master": "QJJQ00000000.1", "refseq_category": "reference genome", "taxid": "1494959", "species_taxid": "1494959", "organism_name": "Pseudogracilibacillus auburnensis", "infraspecific_name": "strain=DSM 28556", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/07", "asm_name": "ASM320197v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003201975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/201/975/GCF_003201975.1_ASM320197v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4779970", "genome_size_ungapped": "4779193", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003201975.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "4492", "protein_coding_gene_count": "4356", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-07", "dateModified": "2018-06-07", "datePublished": "2018-06-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudogracilibacillus auburnensis" ], "sample_taxid": [ "1494959" ], "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": "1.346 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4779970", "Number of Sequences": "39", "Longest Sequences (bp)": "643024", "N50 (bp)": "234488", "Gap Ratio (%)": "0.016381", "GCcontent (%)": "35.6", "Number of CDSs": "4523", "Average Protein Length": "283.0", "Coding Ratio (%)": "80.3", "Number of rRNAs": "4", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudogracilibacillus auburnensis", "strain": "strain=DSM 28556", "accession": "GCA_003201975.1", "taxid": 1494959, "species_taxid": 1494959, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1576, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ornithinibacillus scapharcae", "strain": "strain=TW25", "accession": "GCA_000190475.2", "taxid": 1147159, "species_taxid": 1147159, "relation_to_type": "type", "validated": true, "ani": 77.2282, "matched_fragments": 66, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus kimchii", "strain": "strain=X50", "accession": "GCA_000340475.1", "taxid": 746691, "species_taxid": 746691, "relation_to_type": "type", "validated": true, "ani": 76.9904, "matched_fragments": 71, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus pantothenticus", "strain": "strain=DSM 26", "accession": "GCA_018075365.1", "taxid": 1473, "species_taxid": 1473, "relation_to_type": "type", "validated": true, "ani": 76.7571, "matched_fragments": 95, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus pantothenticus", "strain": "strain=DSM 26", "accession": "GCA_001189575.1", "taxid": 1473, "species_taxid": 1473, "relation_to_type": "type", "validated": true, "ani": 76.6907, "matched_fragments": 97, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Radiobacillus deserti", "strain": "strain=TKL69", "accession": "GCA_007301515.1", "taxid": 2594883, "species_taxid": 2594883, "relation_to_type": "type", "validated": true, "ani": 76.5988, "matched_fragments": 54, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinibacillus halotolerans", "strain": "strain=CGMCC 1.12408", "accession": "GCA_014637405.1", "taxid": 1274357, "species_taxid": 1274357, "relation_to_type": "type", "validated": true, "ani": 76.5922, "matched_fragments": 88, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus pantothenticus", "strain": "strain=DSM 26", "accession": "GCA_900156795.1", "taxid": 1473, "species_taxid": 1473, "relation_to_type": "type", "validated": true, "ani": 76.5864, "matched_fragments": 95, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus ndiopensis", "strain": "strain=Marseille-P3835", "accession": "GCA_900187325.1", "taxid": 2004408, "species_taxid": 2004408, "relation_to_type": "type", "validated": true, "ani": 76.5352, "matched_fragments": 97, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquibacillus sediminis", "strain": "strain=BH258", "accession": "GCA_005870085.1", "taxid": 2574734, "species_taxid": 2574734, "relation_to_type": "type", "validated": true, "ani": 76.3488, "matched_fragments": 53, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus chungangensis", "strain": "strain=CAU 1051", "accession": "GCA_003369565.1", "taxid": 1229152, "species_taxid": 1229152, "relation_to_type": "type", "validated": true, "ani": 76.2643, "matched_fragments": 90, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquibacillus koreensis", "strain": "strain=JCM 12387", "accession": "GCA_025154055.1", "taxid": 279446, "species_taxid": 279446, "relation_to_type": "type", "validated": true, "ani": 76.0891, "matched_fragments": 51, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus arenosus", "strain": "strain=CAU 1183", "accession": "GCA_003369575.1", "taxid": 1229153, "species_taxid": 1229153, "relation_to_type": "type", "validated": true, "ani": 76.0022, "matched_fragments": 68, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Metabacillus bambusae", "strain": "strain=BG109", "accession": "GCA_017497975.1", "taxid": 2795218, "species_taxid": 2795218, "relation_to_type": "type", "validated": true, "ani": 75.8749, "matched_fragments": 67, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salirhabdus euzebyi", "strain": "strain=DSM 19612", "accession": "GCA_014207435.1", "taxid": 394506, "species_taxid": 394506, "relation_to_type": "type", "validated": true, "ani": 75.8296, "matched_fragments": 55, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysinibacillus composti", "strain": "strain=MCCC 1A13240", "accession": "GCA_003856865.1", "taxid": 720633, "species_taxid": 720633, "relation_to_type": "type", "validated": true, "ani": 75.1946, "matched_fragments": 50, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003201975.1", "gtdb_species": "s__Pseudogracilibacillus auburnensis", "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pseudogracilibacillus", "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_000190475.1", "gtdb_species": "s__Ornithinibacillus scapharcae", "ani": 77.2154, "matched_fragments": 66, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus", "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_000340475.1", "gtdb_species": "s__Oceanobacillus kimchii", "ani": 76.9905, "matched_fragments": 72, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_018075365.1", "gtdb_species": "s__Virgibacillus pantothenticus", "ani": 76.7571, "matched_fragments": 95, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCA_019113205.1", "gtdb_species": "s__Pseudogracilibacillus intestinigallinarum", "ani": 76.6969, "matched_fragments": 174, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pseudogracilibacillus", "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_007301515.1", "gtdb_species": "s__Radiobacillus deserti", "ani": 76.6371, "matched_fragments": 55, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Radiobacillus", "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_014637405.1", "gtdb_species": "s__Ornithinibacillus halotolerans", "ani": 76.5511, "matched_fragments": 89, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus", "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_900187325.1", "gtdb_species": "s__Virgibacillus_E ndiopensis", "ani": 76.5294, "matched_fragments": 101, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E", "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_900258515.1", "gtdb_species": "s__Virgibacillus_E sp900258515", "ani": 76.4638, "matched_fragments": 82, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E", "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_009728145.1", "gtdb_species": "s__Ornithinibacillus caprae", "ani": 76.4254, "matched_fragments": 106, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus", "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_016919725.1", "gtdb_species": "s__Virgibacillus sp016919725", "ani": 76.3416, "matched_fragments": 91, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_005870085.1", "gtdb_species": "s__BH258 sp005870085", "ani": 76.3329, "matched_fragments": 53, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258", "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_003612345.1", "gtdb_species": "s__Virgibacillus sp003612345", "ani": 76.2762, "matched_fragments": 77, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus", "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": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001368815.1", "gtdb_species": "s__Paraliobacillus sp001368815", "ani": 76.1874, "matched_fragments": 62, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus", "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_018918075.1", "gtdb_species": "s__MSJ-26 sp018918075", "ani": 76.1091, "matched_fragments": 95, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__MSJ-26", "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_014202495.1", "gtdb_species": "s__Cerasibacillus quisquiliarum", "ani": 76.0886, "matched_fragments": 89, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus", "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_001659985.1", "gtdb_species": "s__Oceanobacillus sp001659985", "ani": 76.0635, "matched_fragments": 80, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus", "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_009389585.1", "gtdb_species": "s__Oceanobacillus sp009389585", "ani": 75.9552, "matched_fragments": 57, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 30.0, "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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Pseudogracilibacillus", "auburnensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }