{ "type": "genome", "identifier": "GCF_900111445.1", "organism": "Oceanobacillus limi", "title": "Oceanobacillus limi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900111445.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216389", "wgs_master": "FOHE00000000.1", "refseq_category": "reference genome", "taxid": "930131", "species_taxid": "930131", "organism_name": "Oceanobacillus limi", "infraspecific_name": "strain=IBRC-M 10780", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2654587897 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900111445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/111/445/GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3913837", "genome_size_ungapped": "3910061", "gc_percent": "37.000000", "replicon_count": "0", "scaffold_count": "51", "contig_count": "51", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900111445.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "4053", "protein_coding_gene_count": "3922", "non_coding_gene_count": "91", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Oceanobacillus limi" ], "sample_taxid": [ "930131" ], "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": "1.108 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)": "3913837", "Number of Sequences": "51", "Longest Sequences (bp)": "421090", "N50 (bp)": "178095", "Gap Ratio (%)": "0.096478", "GCcontent (%)": "37.0", "Number of CDSs": "3982", "Average Protein Length": "274.0", "Coding Ratio (%)": "83.6", "Number of rRNAs": "3", "Number of tRNAs": "73", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ornithinibacillus halophilus", "strain": "strain=IBRC-M 10683", "accession": "GCA_900129485.1", "taxid": 930117, "species_taxid": 930117, "relation_to_type": "type", "validated": true, "ani": 78.1576, "matched_fragments": 258, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinibacillus contaminans", "strain": "strain=DSM 22953", "accession": "GCA_001038425.2", "taxid": 694055, "species_taxid": 694055, "relation_to_type": "type", "validated": true, "ani": 77.8084, "matched_fragments": 185, "total_fragments": 1280, "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": 77.5886, "matched_fragments": 180, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus oceani", "strain": "strain=CGMCC 1.12754", "accession": "GCA_014638995.1", "taxid": 1479511, "species_taxid": 1479511, "relation_to_type": "type", "validated": true, "ani": 77.5547, "matched_fragments": 150, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinibacillus scapharcae", "strain": "strain=TW25", "accession": "GCA_000190475.2", "taxid": 1147159, "species_taxid": 1147159, "relation_to_type": "type", "validated": true, "ani": 77.5522, "matched_fragments": 172, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus profundi", "strain": "strain=P3-H5", "accession": "GCA_002287375.1", "taxid": 2024555, "species_taxid": 2024555, "relation_to_type": "type", "validated": true, "ani": 77.344, "matched_fragments": 187, "total_fragments": 1280, "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": 77.2864, "matched_fragments": 196, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus polygoni", "strain": "strain=SA9", "accession": "GCA_008304605.1", "taxid": 1235259, "species_taxid": 1235259, "relation_to_type": "type", "validated": true, "ani": 77.2793, "matched_fragments": 144, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus massiliensis", "strain": "strain=Vm-5", "accession": "GCA_000723585.1", "taxid": 1462526, "species_taxid": 1462526, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1582, "matched_fragments": 148, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinibacillus gellani", "strain": "strain=LJ137", "accession": "GCA_003730295.1", "taxid": 2293253, "species_taxid": 2293253, "relation_to_type": "type", "validated": true, "ani": 77.1424, "matched_fragments": 111, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquibacillus albus", "strain": "strain=DSM 23711", "accession": "GCA_016908325.1", "taxid": 1168171, "species_taxid": 1168171, "relation_to_type": "type", "validated": true, "ani": 77.1412, "matched_fragments": 92, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus massiliensis", "strain": "strain=Vm-5", "accession": "GCA_014905475.1", "taxid": 1462526, "species_taxid": 1462526, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1033, "matched_fragments": 150, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraliobacillus salinarum", "strain": "strain=G6-18", "accession": "GCA_014083865.1", "taxid": 1158996, "species_taxid": 1158996, "relation_to_type": "type", "validated": true, "ani": 76.9356, "matched_fragments": 68, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus chiguensis", "strain": "strain=CGMCC 1.6496", "accession": "GCA_900129865.1", "taxid": 411959, "species_taxid": 411959, "relation_to_type": "type", "validated": true, "ani": 76.9169, "matched_fragments": 126, "total_fragments": 1280, "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": 76.1086, "matched_fragments": 63, "total_fragments": 1280, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900111445.1", "gtdb_species": "s__Ornithinibacillus limi", "ani": 100.0, "matched_fragments": 1273, "total_fragments": 1280, "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": "conclusive" }, { "accession": "GCF_009728145.1", "gtdb_species": "s__Ornithinibacillus caprae", "ani": 79.2885, "matched_fragments": 462, "total_fragments": 1280, "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_900129485.1", "gtdb_species": "s__Ornithinibacillus halophilus", "ani": 78.1464, "matched_fragments": 256, "total_fragments": 1280, "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_001038425.2", "gtdb_species": "s__Ornithinibacillus contaminans", "ani": 77.7286, "matched_fragments": 187, "total_fragments": 1280, "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_014637405.1", "gtdb_species": "s__Ornithinibacillus halotolerans", "ani": 77.5763, "matched_fragments": 180, "total_fragments": 1280, "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_000190475.1", "gtdb_species": "s__Ornithinibacillus scapharcae", "ani": 77.5345, "matched_fragments": 173, "total_fragments": 1280, "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": 77.3441, "matched_fragments": 156, "total_fragments": 1280, "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_003628445.1", "gtdb_species": "s__Oceanobacillus bengalensis", "ani": 77.2963, "matched_fragments": 154, "total_fragments": 1280, "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_900187325.1", "gtdb_species": "s__Virgibacillus_E ndiopensis", "ani": 77.2721, "matched_fragments": 197, "total_fragments": 1280, "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_016908155.1", "gtdb_species": "s__Oceanobacillus caeni", "ani": 77.2385, "matched_fragments": 130, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.65", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_900166595.1", "gtdb_species": "s__Virgibacillus dokdonensis", "ani": 77.2335, "matched_fragments": 120, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus", "ani_circumscription_radius": 95.5968, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014905415.1", "gtdb_species": "s__Virgibacillus salexigens", "ani": 77.1691, "matched_fragments": 152, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.53", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_003730295.1", "gtdb_species": "s__LJ137 sp003730295", "ani": 77.1424, "matched_fragments": 111, "total_fragments": 1280, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137", "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_900184735.1", "gtdb_species": "s__Ornithinibacillus globulus_B", "ani": 77.1421, "matched_fragments": 210, "total_fragments": 1280, "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_000482485.1", "gtdb_species": "s__Ornithinibacillus globulus", "ani": 77.0839, "matched_fragments": 197, "total_fragments": 1280, "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_014083865.1", "gtdb_species": "s__Paraliobacillus salinarum", "ani": 76.9356, "matched_fragments": 68, "total_fragments": 1280, "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": 76.4942, "matched_fragments": 104, "total_fragments": 1280, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.211, "cell_length": 0.321, "doubling_h": null, "growth_tmp": 30.75, "optimum_tmp": 34.692, "optimum_ph": 8.022, "genome_size": 3913837.0, "gc_content": 37.251, "coding_genes": 3521.75, "rRNA16S_genes": 7.0, "tRNA_genes": 67.0, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.066, "anaerobic_respiration": 0.066, "aerobic_respiration": 0.866, "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": [ "Oceanobacillus", "limi" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }