{ "type": "genome", "identifier": "GCF_016909015.1", "organism": "Gracilibacillus alcaliphilus", "title": "Gracilibacillus alcaliphilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016909015.1", "bioproject": "PRJNA224116", "biosample": "SAMN17619973", "wgs_master": "JAFBFA000000000.1", "refseq_category": "reference genome", "taxid": "1401441", "species_taxid": "1401441", "organism_name": "Gracilibacillus alcaliphilus", "infraspecific_name": "strain=DSM 102988", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/19", "asm_name": "ASM1690901v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_016909015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/909/015/GCF_016909015.1_ASM1690901v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5175195", "genome_size_ungapped": "5175195", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "84", "contig_count": "84", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016909015.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4842", "protein_coding_gene_count": "4680", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-19", "dateModified": "2021-02-19", "datePublished": "2021-02-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Gracilibacillus alcaliphilus" ], "sample_taxid": [ "1401441" ], "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": "1.475 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 6.48, "strain_heterogeneity": 66.67, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5175195", "Number of Sequences": "84", "Longest Sequences (bp)": "346312", "N50 (bp)": "110457", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.0", "Number of CDSs": "4861", "Average Protein Length": "293.5", "Coding Ratio (%)": "82.7", "Number of rRNAs": "4", "Number of tRNAs": "51", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gracilibacillus timonensis", "strain": "strain=Marseille-P2481", "accession": "GCA_900086715.1", "taxid": 1816696, "species_taxid": 1816696, "relation_to_type": "type", "validated": true, "ani": 78.2203, "matched_fragments": 384, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus thailandensis", "strain": "strain=TP2-8", "accession": "GCA_009659515.1", "taxid": 563735, "species_taxid": 563735, "relation_to_type": "type", "validated": true, "ani": 78.0966, "matched_fragments": 233, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus thailandensis", "strain": "strain=TP2-8", "accession": "GCA_010994055.1", "taxid": 563735, "species_taxid": 563735, "relation_to_type": "type", "validated": true, "ani": 78.057, "matched_fragments": 230, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphibacillus sediminis", "strain": "strain=NBRC 103570", "accession": "GCA_001552275.1", "taxid": 360185, "species_taxid": 360185, "relation_to_type": "type", "validated": true, "ani": 77.9287, "matched_fragments": 84, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus lacisalsi", "strain": "strain=DSM 19029", "accession": "GCA_000377765.1", "taxid": 393087, "species_taxid": 393087, "relation_to_type": "type", "validated": true, "ani": 77.7497, "matched_fragments": 239, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus salitolerans", "strain": "strain=SCU50", "accession": "GCA_009650095.1", "taxid": 2663022, "species_taxid": 2663022, "relation_to_type": "type", "validated": true, "ani": 77.6729, "matched_fragments": 242, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus boraciitolerans", "strain": "strain=JCM 21714", "accession": "GCA_000521485.1", "taxid": 307521, "species_taxid": 307521, "relation_to_type": "type", "validated": true, "ani": 77.6551, "matched_fragments": 156, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus saliphilus", "strain": "strain=YIM 91119", "accession": "GCA_010994085.1", "taxid": 543890, "species_taxid": 543890, "relation_to_type": "type", "validated": true, "ani": 77.6407, "matched_fragments": 235, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gracilibacillus orientalis", "strain": "strain=CGMCC 1.4250", "accession": "GCA_900114645.1", "taxid": 334253, "species_taxid": 334253, "relation_to_type": "type", "validated": true, "ani": 77.5358, "matched_fragments": 209, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 6.48, "strain_heterogeneity": 66.67 }, "gtdb_result": [ { "accession": "GCF_016909015.1", "gtdb_species": "s__Gracilibacillus alcaliphilus", "ani": 100.0, "matched_fragments": 1678, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "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": "GCA_900626275.1", "gtdb_species": "s__Gracilibacillus phocaeensis", "ani": 78.2615, "matched_fragments": 390, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001552275.1", "gtdb_species": "s__Amphibacillus_B sediminis", "ani": 77.9287, "matched_fragments": 84, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_B", "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_900143085.1", "gtdb_species": "s__Gracilibacillus kekensis", "ani": 77.8604, "matched_fragments": 197, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "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_001458115.1", "gtdb_species": "s__Gracilibacillus massiliensis", "ani": 77.8319, "matched_fragments": 198, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "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_000377765.1", "gtdb_species": "s__Gracilibacillus lacisalsi", "ani": 77.7761, "matched_fragments": 237, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.88", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_009650095.1", "gtdb_species": "s__Gracilibacillus sp002797295", "ani": 77.6729, "matched_fragments": 242, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003176895.1", "gtdb_species": "s__Gracilibacillus dipsosauri", "ani": 77.6382, "matched_fragments": 144, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900111195.1", "gtdb_species": "s__Gracilibacillus ureilyticus", "ani": 77.6308, "matched_fragments": 135, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "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_900114645.1", "gtdb_species": "s__Gracilibacillus orientalis", "ani": 77.5424, "matched_fragments": 210, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "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_009498735.1", "gtdb_species": "s__Gracilibacillus sp009498735", "ani": 77.3463, "matched_fragments": 157, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus", "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": 77.0398, "matched_fragments": 64, "total_fragments": 1682, "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": -0.45, "cell_length": 0.306, "doubling_h": null, "growth_tmp": 35.0, "optimum_tmp": 35.375, "optimum_ph": 7.531, "genome_size": 4155643.833, "gc_content": 36.8, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 1.0, "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": [ "Gracilibacillus", "alcaliphilus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }