{ "type": "genome", "identifier": "GCF_900113125.1", "organism": "Halobacillus alkaliphilus", "title": "Halobacillus alkaliphilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900113125.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216353", "wgs_master": "FOOG00000000.1", "refseq_category": "reference genome", "taxid": "396056", "species_taxid": "396056", "organism_name": "Halobacillus alkaliphilus", "infraspecific_name": "strain=FP5", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2654587900 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900113125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/113/125/GCF_900113125.1_IMG-taxon_2654587900_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": "4092525", "genome_size_ungapped": "4088447", "gc_percent": "41.500000", "replicon_count": "0", "scaffold_count": "93", "contig_count": "93", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900113125.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "4086", "protein_coding_gene_count": "3952", "non_coding_gene_count": "78", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Halobacillus alkaliphilus" ], "sample_taxid": [ "396056" ], "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": "1.171 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)": "4092525", "Number of Sequences": "93", "Longest Sequences (bp)": "281660", "N50 (bp)": "70870", "Gap Ratio (%)": "0.099645", "GCcontent (%)": "41.6", "Number of CDSs": "4022", "Average Protein Length": "282.0", "Coding Ratio (%)": "83.1", "Number of rRNAs": "7", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halobacillus alkaliphilus", "strain": "strain=FP5", "accession": "GCA_900113125.1", "taxid": 396056, "species_taxid": 396056, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1311, "total_fragments": 1317, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halobacillus halophilus", "strain": "strain=type strain: DSM 2266", "accession": "GCA_000284515.1", "taxid": 1570, "species_taxid": 1570, "relation_to_type": "type", "validated": true, "ani": 91.688, "matched_fragments": 1162, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus dabanensis", "strain": "strain=CGMCC 1.3704", "accession": "GCA_900114165.1", "taxid": 240302, "species_taxid": 240302, "relation_to_type": "type", "validated": true, "ani": 78.9039, "matched_fragments": 264, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus locisalis", "strain": "strain=KCTC 3788", "accession": "GCA_013694105.1", "taxid": 220753, "species_taxid": 220753, "relation_to_type": "type", "validated": true, "ani": 78.7016, "matched_fragments": 223, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus salinus", "strain": "strain=HSL-3", "accession": "GCA_004684905.1", "taxid": 192814, "species_taxid": 192814, "relation_to_type": "type", "validated": true, "ani": 78.5292, "matched_fragments": 193, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus litoralis", "strain": "strain=SL-4", "accession": "GCA_009856445.1", "taxid": 45668, "species_taxid": 45668, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2723, "matched_fragments": 265, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus faecis", "strain": "strain=NBRC 103569", "accession": "GCA_007991335.1", "taxid": 360184, "species_taxid": 360184, "relation_to_type": "type", "validated": true, "ani": 78.2299, "matched_fragments": 257, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus andaensis", "strain": "strain=CGMCC 1.12153", "accession": "GCA_014636475.1", "taxid": 1176239, "species_taxid": 1176239, "relation_to_type": "type", "validated": true, "ani": 77.9239, "matched_fragments": 195, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus kuroshimensis", "strain": "strain=DSM 18393", "accession": "GCA_000425705.1", "taxid": 302481, "species_taxid": 302481, "relation_to_type": "type", "validated": true, "ani": 77.8906, "matched_fragments": 216, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halobacillus andaensis", "strain": "strain=DSM 25866", "accession": "GCA_017874135.1", "taxid": 1176239, "species_taxid": 1176239, "relation_to_type": "type", "validated": true, "ani": 77.8761, "matched_fragments": 192, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salimicrobium halophilum", "strain": "strain=DSM 4771", "accession": "GCA_900100295.1", "taxid": 86666, "species_taxid": 86666, "relation_to_type": "type", "validated": true, "ani": 77.52, "matched_fragments": 83, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terribacillus aidingensis", "strain": "strain=CGMCC 1.8913", "accession": "GCA_900215625.1", "taxid": 586416, "species_taxid": 586416, "relation_to_type": "type", "validated": true, "ani": 77.1752, "matched_fragments": 50, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sediminibacillus halophilus", "strain": "strain=CGMCC 1.6199", "accession": "GCA_900103695.1", "taxid": 482461, "species_taxid": 482461, "relation_to_type": "type", "validated": true, "ani": 77.164, "matched_fragments": 53, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus indicus", "strain": "strain=P2-C2", "accession": "GCA_002266285.1", "taxid": 2024554, "species_taxid": 2024554, "relation_to_type": "type", "validated": true, "ani": 76.6065, "matched_fragments": 52, "total_fragments": 1317, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900113125.1", "gtdb_species": "s__Halobacillus alkaliphilus", "ani": 100.0, "matched_fragments": 1311, "total_fragments": 1317, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus", "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_000284515.1", "gtdb_species": "s__Halobacillus halophilus", "ani": 91.7152, "matched_fragments": 1160, "total_fragments": 1317, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900114165.1", "gtdb_species": "s__Halobacillus dabanensis", "ani": 78.8709, "matched_fragments": 266, "total_fragments": 1317, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus", "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_002097535.1", "gtdb_species": "s__Halobacillus mangrovi", "ani": 78.7998, "matched_fragments": 328, 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"d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.79", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900240285.1", "gtdb_species": "s__Halobacillus_A sp900240285", "ani": 77.8304, "matched_fragments": 164, "total_fragments": 1317, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.195, "cell_length": 0.195, "doubling_h": -0.327, "growth_tmp": 32.0, "optimum_tmp": 37.0, "optimum_ph": 9.0, "genome_size": 4092525.0, "gc_content": 43.292, "coding_genes": 3983.0, "rRNA16S_genes": 7.0, "tRNA_genes": 67.5, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.8, "range_salinity": 1.0, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Halobacillus", "alkaliphilus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }