{ "type": "genome", "identifier": "GCF_900155625.1", "organism": "Virgibacillus dakarensis", "title": "Virgibacillus dakarensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900155625.1", "bioproject": "PRJNA224116", "biosample": "SAMEA48328168", "wgs_master": "FUHS00000000.1", "refseq_category": "reference genome", "taxid": "1917889", "species_taxid": "1917889", "organism_name": "Virgibacillus dakarensis", "infraspecific_name": "strain=Marseille-P3469T", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/02/08", "asm_name": "ASM90015562v1", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900155625.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/155/625/GCF_900155625.1_ASM90015562v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4753046", "genome_size_ungapped": "4752643", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900155625.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4717", "protein_coding_gene_count": "4497", "non_coding_gene_count": "86", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-02-08", "dateModified": "2017-02-08", "datePublished": "2017-02-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Virgibacillus dakarensis" ], "sample_taxid": [ "1917889" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.343 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)": "4753046", "Number of Sequences": "6", "Longest Sequences (bp)": "2860113", "N50 (bp)": "2860113", "Gap Ratio (%)": "0.008542", "GCcontent (%)": "39.7", "Number of CDSs": "4677", "Average Protein Length": "277.5", "Coding Ratio (%)": "81.9", "Number of rRNAs": "12", "Number of tRNAs": "65", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Virgibacillus dakarensis", "strain": "strain=Marseille-P3469", "accession": "GCA_900155625.1", "taxid": 1917889, "species_taxid": 1917889, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1579, "total_fragments": 1581, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Oceanobacillus massiliensis", "strain": "strain=Ndiop", "accession": "GCA_000285495.1", "taxid": 1465765, "species_taxid": 1465765, "relation_to_type": "type", "validated": true, "ani": 78.2886, "matched_fragments": 120, "total_fragments": 1581, "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": 78.2815, "matched_fragments": 316, "total_fragments": 1581, "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": 78.1711, "matched_fragments": 154, "total_fragments": 1581, "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": 78.0969, "matched_fragments": 147, "total_fragments": 1581, "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": 77.8503, "matched_fragments": 150, "total_fragments": 1581, "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": 77.8042, "matched_fragments": 315, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraliobacillus ryukyuensis", "strain": "strain=DSM 15140", "accession": "GCA_003315295.1", "taxid": 200904, "species_taxid": 200904, "relation_to_type": "type", "validated": true, "ani": 77.7215, "matched_fragments": 54, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus ihumii", "strain": "strain=Marseille-Q1233", "accession": "GCA_902726655.1", "taxid": 2686091, "species_taxid": 2686091, "relation_to_type": "type", "validated": true, "ani": 77.3548, "matched_fragments": 180, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus salinisoli", "strain": "strain=YIM B00359", "accession": "GCA_009733865.1", "taxid": 2678611, "species_taxid": 2678611, "relation_to_type": "type", "validated": true, "ani": 77.2687, "matched_fragments": 143, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus rekensis", "strain": "strain=PT-11", "accession": "GCA_002153375.1", "taxid": 937927, "species_taxid": 937927, "relation_to_type": "type", "validated": true, "ani": 77.2082, "matched_fragments": 131, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentibacillus halodurans", "strain": "strain=CGMCC 1.3702", "accession": "GCA_900112045.1", "taxid": 237679, "species_taxid": 237679, "relation_to_type": "type", "validated": true, "ani": 77.1911, "matched_fragments": 143, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus litoralis", "strain": "strain=DSM 21085", "accession": "GCA_017873675.1", "taxid": 578221, "species_taxid": 578221, "relation_to_type": "type", "validated": true, "ani": 77.0986, "matched_fragments": 198, "total_fragments": 1581, "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": 77.0773, "matched_fragments": 50, "total_fragments": 1581, "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": 76.9958, "matched_fragments": 109, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus subterraneus", "strain": "strain=CGMCC 1.7734", "accession": "GCA_900110695.1", "taxid": 621109, "species_taxid": 621109, "relation_to_type": "type", "validated": true, "ani": 76.9459, "matched_fragments": 180, "total_fragments": 1581, "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": 76.7412, "matched_fragments": 68, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus sojae", "strain": "strain=NBRC 105379", "accession": "GCA_007991515.1", "taxid": 582851, "species_taxid": 582851, "relation_to_type": "type", "validated": true, "ani": 76.4803, "matched_fragments": 81, "total_fragments": 1581, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_014642895.1", "gtdb_species": "s__Virgibacillus_E populi", "ani": 98.8836, "matched_fragments": 1257, "total_fragments": 1581, "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": "98.98", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_900258515.1", "gtdb_species": "s__Virgibacillus_E sp900258515", "ani": 78.8129, "matched_fragments": 515, "total_fragments": 1581, "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_900187325.1", "gtdb_species": "s__Virgibacillus_E ndiopensis", "ani": 78.2919, "matched_fragments": 314, "total_fragments": 1581, "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_000285495.1", "gtdb_species": "s__Oceanobacillus massiliensis", "ani": 78.2783, "matched_fragments": 121, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus", "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_008304605.1", "gtdb_species": "s__Oceanobacillus polygoni", "ani": 78.1334, "matched_fragments": 151, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus", "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_014905415.1", "gtdb_species": "s__Virgibacillus salexigens", "ani": 78.1008, "matched_fragments": 162, "total_fragments": 1581, "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_014638995.1", "gtdb_species": "s__Virgibacillus_E oceani", "ani": 77.7946, "matched_fragments": 314, "total_fragments": 1581, "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_000612865.1", "gtdb_species": "s__Virgibacillus picturae", "ani": 77.7857, "matched_fragments": 124, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003315295.1", "gtdb_species": "s__Paraliobacillus ryukyuensis", "ani": 77.7215, "matched_fragments": 54, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.18", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016919725.1", "gtdb_species": "s__Virgibacillus sp016919725", "ani": 77.6005, "matched_fragments": 151, "total_fragments": 1581, "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_902726655.1", "gtdb_species": "s__Lentibacillus ihumii", "ani": 77.471, "matched_fragments": 179, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus", "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_900111445.1", "gtdb_species": "s__Ornithinibacillus limi", "ani": 77.3161, "matched_fragments": 137, "total_fragments": 1581, "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_009733865.1", "gtdb_species": "s__Oceanobacillus salinisoli", "ani": 77.2921, "matched_fragments": 143, "total_fragments": 1581, "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_900112045.1", "gtdb_species": "s__Lentibacillus halodurans", "ani": 77.1553, "matched_fragments": 145, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus", "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_017873675.1", "gtdb_species": "s__Lentibacillus litoralis", "ani": 77.0975, "matched_fragments": 198, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus", "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": 77.0773, "matched_fragments": 50, "total_fragments": 1581, "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_003730295.1", "gtdb_species": "s__LJ137 sp003730295", "ani": 76.9742, "matched_fragments": 110, "total_fragments": 1581, "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": "GCA_004145795.1", "gtdb_species": "s__Lentibacillus lipolyticus", "ani": 76.6842, "matched_fragments": 106, "total_fragments": 1581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus", "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": -0.325, "cell_length": 0.349, "doubling_h": 0.096, "growth_tmp": 29.803, "optimum_tmp": 33.233, "optimum_ph": 7.46, "genome_size": 3934850.666, "gc_content": 37.11, "coding_genes": 3813.0, "rRNA16S_genes": 7.5, "tRNA_genes": 62.333, "gram_stain": 1.0, "sporulation": 1.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.136, "anaerobic_respiration": 0.09, "aerobic_respiration": 0.772, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Virgibacillus", "dakarensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }