{ "type": "genome", "identifier": "GCF_000307165.1", "organism": "Amphibacillus xylanus NBRC 15112", "title": "Amphibacillus xylanus NBRC 15112", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000307165.1", "bioproject": "PRJNA224116", "biosample": "SAMD00061112", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "698758", "species_taxid": "1449", "organism_name": "Amphibacillus xylanus NBRC 15112", "infraspecific_name": "strain=NBRC 15112", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/10/01", "asm_name": "ASM30716v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_000307165.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/307/165/GCF_000307165.1_ASM30716v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2569486", "genome_size_ungapped": "2569486", "gc_percent": "35.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000307165.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "2481", "protein_coding_gene_count": "2355", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-10-01", "dateModified": "2012-10-01", "datePublished": "2012-10-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Amphibacillus xylanus NBRC 15112" ], "sample_taxid": [ "698758" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.721 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)": "2569486", "Number of Sequences": "1", "Longest Sequences (bp)": "2569486", "N50 (bp)": "2569486", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.7", "Number of CDSs": "2435", "Average Protein Length": "298.6", "Coding Ratio (%)": "84.9", "Number of rRNAs": "18", "Number of tRNAs": "55", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amphibacillus xylanus", "strain": "strain=NBRC 15112", "accession": "GCA_000307165.1", "taxid": 1449, "species_taxid": 1449, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 856, "total_fragments": 856, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paraliobacillus zengyii", "strain": "strain=X-1125", "accession": "GCA_003268595.1", "taxid": 2213194, "species_taxid": 2213194, "relation_to_type": "type", "validated": true, "ani": 78.8149, "matched_fragments": 74, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cerasibacillus quisquiliarum", "strain": "strain=DSM 15825", "accession": "GCA_014202495.1", "taxid": 227865, "species_taxid": 227865, "relation_to_type": "type", "validated": true, "ani": 78.1422, "matched_fragments": 51, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphibacillus marinus", "strain": "strain=CGMCC 1.10434", "accession": "GCA_900110345.1", "taxid": 872970, "species_taxid": 872970, "relation_to_type": "type", "validated": true, "ani": 77.3947, 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"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": 77.0441, "matched_fragments": 62, "total_fragments": 856, "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": 76.8407, "matched_fragments": 73, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" }, { "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": 76.6941, "matched_fragments": 55, "total_fragments": 856, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000307165.1", "gtdb_species": "s__Amphibacillus xylanus", "ani": 100.0, "matched_fragments": 856, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.98", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_012838505.1", "gtdb_species": "s__Amphibacillus sp012838505", "ani": 80.0778, "matched_fragments": 346, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", 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"status": "-" }, { "accession": "GCF_900110345.1", "gtdb_species": "s__Amphibacillus_D marinus", "ani": 77.4069, "matched_fragments": 90, "total_fragments": 856, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D", "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_001368815.1", "gtdb_species": "s__Paraliobacillus sp001368815", "ani": 77.3883, "matched_fragments": 70, "total_fragments": 856, "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_000306965.1", 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"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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.046, "doubling_h": 0.364, "growth_tmp": 37.0, "optimum_tmp": 32.5, "optimum_ph": 9.0, "genome_size": 2569486.8, "gc_content": 35.7, "coding_genes": 2351.0, "rRNA16S_genes": 6.0, "tRNA_genes": 55.0, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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": [ "Amphibacillus", "xylanus", "NBRC", "15112" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }