{ "type": "genome", "identifier": "GCF_001420645.1", "organism": "Alkalicoccobacillus plakortidis", "title": "Alkalicoccobacillus plakortidis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Fujian Academy of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001420645.1", "bioproject": "PRJNA224116", "biosample": "SAMN04038056", "wgs_master": "LJJD00000000.1", "refseq_category": "reference genome", "taxid": "444060", "species_taxid": "444060", "organism_name": "Alkalicoccobacillus plakortidis", "infraspecific_name": "strain=DSM 19153", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/10/30", "asm_name": "ASM142064v1", "asm_submitter": "Fujian Academy of Agricultural Sciences", "gbrs_paired_asm": "GCA_001420645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/420/645/GCF_001420645.1_ASM142064v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3967762", "genome_size_ungapped": "3967296", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "44", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001420645.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "4143", "protein_coding_gene_count": "4032", "non_coding_gene_count": "82", "pubmed_id": "26847896" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-10-30", "dateModified": "2015-10-30", "datePublished": "2015-10-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Alkalicoccobacillus plakortidis" ], "sample_taxid": [ "444060" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.129 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)": "3967762", "Number of Sequences": "44", "Longest Sequences (bp)": "535841", "N50 (bp)": "227279", "Gap Ratio (%)": "0.012450", "GCcontent (%)": "39.8", "Number of CDSs": "4069", "Average Protein Length": "287.1", "Coding Ratio (%)": "88.3", "Number of rRNAs": "5", "Number of tRNAs": "71", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Alkalihalobacillus xiaoxiensis", "strain": "strain=DSM 21943", "accession": "GCA_016907895.1", "taxid": 766895, "species_taxid": 766895, "relation_to_type": "type", "validated": true, "ani": 78.7226, "matched_fragments": 279, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacillus patagoniensis", "strain": "strain=DSM 16117", "accession": "GCA_002019705.1", "taxid": 228576, "species_taxid": 228576, "relation_to_type": "type", "validated": true, "ani": 78.2663, "matched_fragments": 255, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacillus krulwichiae", "strain": "strain=AM31D", "accession": "GCA_002109385.1", "taxid": 199441, "species_taxid": 199441, "relation_to_type": "type", "validated": true, "ani": 77.2911, "matched_fragments": 76, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerobacillus alkalilacustris", "strain": "strain=DSM 18345", "accession": "GCA_001866005.1", "taxid": 393763, "species_taxid": 393763, "relation_to_type": "type", "validated": true, "ani": 77.2753, "matched_fragments": 51, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacillus krulwichiae", "strain": "strain=NBRC 102362", "accession": "GCA_001591945.1", "taxid": 199441, "species_taxid": 199441, "relation_to_type": "type", "validated": true, "ani": 77.2723, "matched_fragments": 76, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacillus alcalophilus", "strain": "strain=AV1934", "accession": "GCA_000292245.2", "taxid": 1445, "species_taxid": 1445, "relation_to_type": "type", "validated": true, "ani": 77.0522, "matched_fragments": 87, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus alkalicellulosilyticus", "strain": "strain=FJAT-44921", "accession": "GCA_002019795.1", "taxid": 1912214, "species_taxid": 1912214, "relation_to_type": "type", "validated": true, "ani": 76.9024, "matched_fragments": 59, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerobacillus alkaliphilus", "strain": "strain=B16-10", "accession": "GCA_004116265.1", "taxid": 1548597, "species_taxid": 1548597, "relation_to_type": "type", "validated": true, "ani": 76.8711, "matched_fragments": 52, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anaerobacillus isosaccharinicus", "strain": "strain=NB2006", "accession": "GCA_001866075.3", "taxid": 1532552, "species_taxid": 1532552, "relation_to_type": "type", "validated": true, "ani": 76.8372, "matched_fragments": 52, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacterium alkalinitrilicum", "strain": "strain=DSM 22532", "accession": "GCA_002019605.1", "taxid": 427920, "species_taxid": 427920, "relation_to_type": "type", "validated": true, "ani": 76.8147, "matched_fragments": 60, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalophilus marmarensis", "strain": "strain=DSM 21297", "accession": "GCA_000474275.2", "taxid": 521377, "species_taxid": 521377, "relation_to_type": "type", "validated": true, "ani": 76.7735, "matched_fragments": 72, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacillus alcalophilus", "strain": "strain=CGMCC 1.3604", "accession": "GCA_004802515.1", "taxid": 1445, "species_taxid": 1445, "relation_to_type": "type", "validated": true, "ani": 76.6505, "matched_fragments": 75, "total_fragments": 1299, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002019765.1", "gtdb_species": "s__Bacillus_H oshimensis", "ani": 99.9948, "matched_fragments": 1299, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.65", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_007725405.1", "gtdb_species": "s__Bacillus_H miscanthi", "ani": 91.1256, "matched_fragments": 1178, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "99.10", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900197585.1", "gtdb_species": "s__Bacillus_H sp900197585", "ani": 80.1965, "matched_fragments": 579, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H", "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_016907895.1", "gtdb_species": "s__Bacillus_H xiaoxiensis", "ani": 78.7002, "matched_fragments": 279, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.73", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002019705.1", "gtdb_species": "s__Bacillus_H patagoniensis", "ani": 78.2699, "matched_fragments": 256, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H", "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": "GCA_001310375.1", "gtdb_species": "s__Bacillus_H sp001310375", "ani": 78.1989, "matched_fragments": 231, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H", "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_000005825.2", "gtdb_species": "s__Bacillus_S pseudofirmus", "ani": 77.3373, "matched_fragments": 78, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S", "ani_circumscription_radius": 95.9507, "mean_intra_species_ani": "97.22", "min_intra_species_ani": "97.22", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_001038565.1", "gtdb_species": "s__Alkalihalobacillus pseudalcaliphilus", "ani": 77.3108, "matched_fragments": 76, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus", "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_002109385.1", "gtdb_species": "s__Bacillus_L krulwichiae", "ani": 77.3001, "matched_fragments": 77, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L", "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_000513095.1", "gtdb_species": "s__Bacillus_L wakoensis", "ani": 77.1405, "matched_fragments": 75, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000292245.2", "gtdb_species": "s__Alkalihalobacillus alcalophilus", "ani": 77.051, "matched_fragments": 87, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.82", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002019795.1", "gtdb_species": "s__Bacillus_AO alkalicellulosilyticus", "ani": 76.8758, "matched_fragments": 60, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO", "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_001866075.3", "gtdb_species": "s__Anaerobacillus isosaccharinicus", "ani": 76.8372, "matched_fragments": 52, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus", "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_000474275.2", "gtdb_species": "s__Bacillus_S marmarensis", "ani": 76.7995, "matched_fragments": 71, "total_fragments": 1299, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S", "ani_circumscription_radius": 95.9507, "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": null, "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": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Alkalicoccobacillus", "plakortidis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }