{ "type": "genome", "identifier": "GCF_002211785.1", "organism": "Francisella halioticida", "title": "Francisella halioticida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Swedish Defence Research Agency (FOI)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002211785.1", "bioproject": "PRJNA224116", "biosample": "SAMN07207140", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "549298", "species_taxid": "549298", "organism_name": "Francisella halioticida", "infraspecific_name": "strain=DSM 23729", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/06/30", "asm_name": "ASM221178v1", "asm_submitter": "Swedish Defence Research Agency (FOI)", "gbrs_paired_asm": "GCA_002211785.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/211/785/GCF_002211785.1_ASM221178v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2197430", "genome_size_ungapped": "2197430", "gc_percent": "31.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002211785.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2459", "protein_coding_gene_count": "2261", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-06-30", "dateModified": "2017-06-30", "datePublished": "2017-06-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Francisella halioticida" ], "sample_taxid": [ "549298" ], "sample_host_organism": [ "Haliotis gigantea" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "0.591 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2197430", "Number of Sequences": "1", "Longest Sequences (bp)": "2197430", "N50 (bp)": "2197430", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "31.2", "Number of CDSs": "2443", "Average Protein Length": "258.7", "Coding Ratio (%)": "86.3", "Number of rRNAs": "10", "Number of tRNAs": "40", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Francisella halioticida", "strain": "strain=DSM 23729", "accession": "GCA_002211785.1", "taxid": 549298, "species_taxid": 549298, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 729, "total_fragments": 732, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Francisella uliginis", "strain": "strain=TX07-7310", "accession": "GCA_001895265.1", "taxid": 573570, "species_taxid": 573570, "relation_to_type": "type", "validated": true, "ani": 84.4818, "matched_fragments": 526, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella salina", "strain": "strain=TX07-7308", "accession": "GCA_000219045.1", "taxid": 573569, "species_taxid": 573569, "relation_to_type": "type", "validated": true, "ani": 79.3874, "matched_fragments": 291, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella noatunensis subsp. noatunensis", "strain": "strain=2005/50/F292-6", "accession": "GCA_009823375.1", "taxid": 360196, "species_taxid": 657445, "relation_to_type": "type", "validated": true, "ani": 79.3497, "matched_fragments": 251, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella tularensis subsp. novicida", "strain": "strain=U112", "accession": "GCA_000014645.1", "taxid": 264, "species_taxid": 263, "relation_to_type": "type", "validated": true, "ani": 79.338, "matched_fragments": 320, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella opportunistica", "strain": "strain=PA05-1188", "accession": "GCA_003347135.1", "taxid": 2016517, "species_taxid": 2016517, "relation_to_type": "type", "validated": true, "ani": 79.2859, "matched_fragments": 275, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella hispaniensis", "strain": "strain=CCUG 58020", "accession": "GCA_001885235.1", "taxid": 622488, "species_taxid": 622488, "relation_to_type": "type", "validated": true, "ani": 79.2565, "matched_fragments": 309, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella philomiragia", "strain": "strain=O#319L", "accession": "GCA_000833455.1", "taxid": 28110, "species_taxid": 28110, "relation_to_type": "type", "validated": true, "ani": 79.2333, "matched_fragments": 298, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella hispaniensis", "strain": "strain=CCUG 58020", "accession": "GCA_001608445.1", "taxid": 622488, "species_taxid": 622488, "relation_to_type": "type", "validated": true, "ani": 79.1275, "matched_fragments": 304, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Francisella philomiragia", "strain": "strain=ATCC 25015", "accession": "GCA_000156715.1", "taxid": 28110, "species_taxid": 28110, "relation_to_type": "type", "validated": true, "ani": 78.9902, "matched_fragments": 307, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allofrancisella guangzhouensis", "strain": "strain=08HL01032", "accession": "GCA_000815225.1", "taxid": 594679, "species_taxid": 594679, "relation_to_type": "type", "validated": true, "ani": 78.1886, "matched_fragments": 192, "total_fragments": 732, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002211785.1", "gtdb_species": "s__Francisella halioticida", "ani": 100.0, "matched_fragments": 729, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.38", "min_intra_species_ani": "99.38", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001895265.1", "gtdb_species": "s__Francisella uliginis", "ani": 84.5225, "matched_fragments": 526, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "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_012224145.1", "gtdb_species": "s__Francisella sp012224145", "ani": 83.3484, "matched_fragments": 501, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "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_008711465.1", "gtdb_species": "s__Francisella sp008711465", "ani": 82.8945, "matched_fragments": 520, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "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_000764555.1", "gtdb_species": "s__Francisella sp000764555", "ani": 79.5444, "matched_fragments": 302, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "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_001885235.1", "gtdb_species": "s__Francisella hispaniensis", "ani": 79.2442, "matched_fragments": 308, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003347135.1", "gtdb_species": "s__Francisella opportunistica", "ani": 79.1552, "matched_fragments": 287, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.85", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000156715.1", "gtdb_species": "s__Francisella philomiragia", "ani": 79.0056, "matched_fragments": 306, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.38", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 49, "status": "-" }, { "accession": "GCF_007923265.1", "gtdb_species": "s__Francisella salimarina", "ani": 78.9858, "matched_fragments": 301, "total_fragments": 732, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.26", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 8, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.477, "growth_tmp": 20.0, "optimum_tmp": 36.75, "optimum_ph": 6.3, "genome_size": 2197430.0, "gc_content": 31.2, "coding_genes": 2096.0, "rRNA16S_genes": 3.0, "tRNA_genes": 40.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.5, "coccus_cell_shape": 0.5, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Francisella", "halioticida" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }