{ "type": "genome", "identifier": "GCF_018310345.1", "organism": "Ornithinibacillus massiliensis", "title": "Ornithinibacillus massiliensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "IHU Mediterranee Infection", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018310345.1", "bioproject": "PRJNA224116", "biosample": "SAMN18982120", "wgs_master": "JAGXBY000000000.1", "refseq_category": "reference genome", "taxid": "1944633", "species_taxid": "1944633", "organism_name": "Ornithinibacillus massiliensis", "infraspecific_name": "strain=Marseille-P3601", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/08", "asm_name": "ASM1831034v1", "asm_submitter": "IHU Mediterranee Infection", "gbrs_paired_asm": "GCA_018310345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/310/345/GCF_018310345.1_ASM1831034v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3865210", "genome_size_ungapped": "3865010", "gc_percent": "37.000000", "replicon_count": "0", "scaffold_count": "16", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018310345.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "3857", "protein_coding_gene_count": "3736", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-08", "dateModified": "2021-05-08", "datePublished": "2021-05-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Ornithinibacillus massiliensis" ], "sample_taxid": [ "1944633" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Senegal: Dakar" ], "sample_host_location_id": [], "data_size": "1.094 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)": "3865210", "Number of Sequences": "16", "Longest Sequences (bp)": "871854", "N50 (bp)": "704178", "Gap Ratio (%)": "0.005174", "GCcontent (%)": "37.0", "Number of CDSs": "3813", "Average Protein Length": "286.0", "Coding Ratio (%)": "84.6", "Number of rRNAs": "8", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Ornithinibacillus massiliensis", "strain": "strain=Marseille-P3601", "accession": "GCA_018310345.1", "taxid": 1944633, "species_taxid": 1944633, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1276, "total_fragments": 1279, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Ornithinibacillus scapharcae", "strain": "strain=TW25", "accession": "GCA_000190475.2", "taxid": 1147159, "species_taxid": 1147159, "relation_to_type": "type", "validated": true, "ani": 78.9946, "matched_fragments": 394, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinibacillus halotolerans", "strain": "strain=CGMCC 1.12408", "accession": "GCA_014637405.1", "taxid": 1274357, "species_taxid": 1274357, "relation_to_type": "type", "validated": true, "ani": 78.5828, "matched_fragments": 352, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinibacillus contaminans", "strain": "strain=DSM 22953", "accession": "GCA_001038425.2", "taxid": 694055, "species_taxid": 694055, "relation_to_type": "type", "validated": true, "ani": 78.5741, "matched_fragments": 351, "total_fragments": 1279, "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": 77.8376, "matched_fragments": 122, "total_fragments": 1279, "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": 77.6901, "matched_fragments": 192, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus arenosus", "strain": "strain=CAU 1183", "accession": "GCA_003369575.1", "taxid": 1229153, "species_taxid": 1229153, "relation_to_type": "type", "validated": true, "ani": 77.2593, "matched_fragments": 114, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus bengalensis", "strain": "strain=MCCC 1K00260", "accession": "GCA_003628445.1", "taxid": 1435466, "species_taxid": 1435466, "relation_to_type": "type", "validated": true, "ani": 77.1907, "matched_fragments": 143, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus piezotolerans", "strain": "strain=YLB-02", "accession": "GCA_003665065.1", "taxid": 2448030, "species_taxid": 2448030, "relation_to_type": "type", "validated": true, "ani": 77.01, "matched_fragments": 120, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacillus halotolerans", "strain": "strain=YIM 98839", "accession": "GCA_010993955.1", "taxid": 2663380, "species_taxid": 2663380, "relation_to_type": "type", "validated": true, "ani": 76.9568, "matched_fragments": 127, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus halotolerans", "strain": "strain=DSM 25060", "accession": "GCA_016908515.1", "taxid": 1071053, "species_taxid": 1071053, "relation_to_type": "type", "validated": true, "ani": 76.917, "matched_fragments": 106, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Virgibacillus natechei", "strain": "strain=DSM 25609", "accession": "GCA_017874115.1", "taxid": 1216297, "species_taxid": 1216297, "relation_to_type": "type", "validated": true, "ani": 76.6335, "matched_fragments": 103, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraliobacillus sediminis", "strain": "strain=126C4", "accession": "GCA_003426055.1", "taxid": 1885916, "species_taxid": 1885916, "relation_to_type": "type", "validated": true, "ani": 76.0945, "matched_fragments": 51, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018310345.1", "gtdb_species": "s__Ornithinibacillus massiliensis", "ani": 100.0, "matched_fragments": 1276, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001038485.1", "gtdb_species": "s__Ornithinibacillus californiensis", "ani": 79.5977, "matched_fragments": 490, "total_fragments": 1279, "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_000577245.1", "gtdb_species": "s__Ornithinibacillus sp000577245", "ani": 79.0026, "matched_fragments": 458, "total_fragments": 1279, "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_000190475.1", "gtdb_species": "s__Ornithinibacillus scapharcae", "ani": 78.9882, "matched_fragments": 396, "total_fragments": 1279, "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_000482485.1", "gtdb_species": "s__Ornithinibacillus globulus", "ani": 78.9214, "matched_fragments": 432, "total_fragments": 1279, "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_900184735.1", "gtdb_species": "s__Ornithinibacillus globulus_B", "ani": 78.7631, "matched_fragments": 430, "total_fragments": 1279, "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_001038425.2", "gtdb_species": "s__Ornithinibacillus contaminans", "ani": 78.5698, "matched_fragments": 352, "total_fragments": 1279, "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_900240995.1", "gtdb_species": "s__OESV01 sp900240995", "ani": 76.8244, "matched_fragments": 53, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__OESV01", "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": -0.252, "cell_length": 0.56, "doubling_h": null, "growth_tmp": 31.0, "optimum_tmp": 34.875, "optimum_ph": 7.666, "genome_size": 3668847.75, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.666, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Ornithinibacillus", "massiliensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }