{ "type": "genome", "identifier": "GCF_011392115.1", "organism": "Flavobacterium difficile", "title": "Flavobacterium difficile", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Kaohsiung University of Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011392115.1", "bioproject": "PRJNA224116", "biosample": "SAMN14090729", "wgs_master": "JAAJBT000000000.1", "refseq_category": "reference genome", "taxid": "2709659", "species_taxid": "2709659", "organism_name": "Flavobacterium difficile", "infraspecific_name": "strain=KDG-16", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/17", "asm_name": "ASM1139211v1", "asm_submitter": "National Kaohsiung University of Science and Technology", "gbrs_paired_asm": "GCA_011392115.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/392/115/GCF_011392115.1_ASM1139211v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2955906", "genome_size_ungapped": "2955906", "gc_percent": "31.500000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011392115.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "2670", "protein_coding_gene_count": "2597", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-17", "dateModified": "2020-03-17", "datePublished": "2020-03-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Flavobacterium difficile" ], "sample_taxid": [ "2709659" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Taiwan" ], "sample_host_location_id": [], "data_size": "0.813 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)": "2955906", "Number of Sequences": "33", "Longest Sequences (bp)": "667766", "N50 (bp)": "307762", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "31.6", "Number of CDSs": "2596", "Average Protein Length": "338.2", "Coding Ratio (%)": "89.1", "Number of rRNAs": "2", "Number of tRNAs": "41", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Flavobacterium difficile", "strain": "strain=KDG-16", "accession": "GCA_011392115.1", "taxid": 2709659, "species_taxid": 2709659, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 973, "total_fragments": 975, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium bernardetii", "strain": "strain=F-372", "accession": "GCA_011305415.1", "taxid": 2813823, "species_taxid": 2813823, "relation_to_type": "type", "validated": true, "ani": 84.9486, "matched_fragments": 712, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium terrigena", "strain": "strain=DSM 17934", "accession": "GCA_900108955.1", "taxid": 402734, "species_taxid": 402734, "relation_to_type": "type", "validated": true, "ani": 84.3375, "matched_fragments": 691, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium urocaniciphilum", "strain": "strain=DSM 27078", "accession": "GCA_900110615.1", "taxid": 1299341, "species_taxid": 1299341, "relation_to_type": "type", "validated": true, "ani": 81.3118, "matched_fragments": 617, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium channae", "strain": "strain=KSM-R2A30", "accession": "GCA_021172165.1", "taxid": 2897181, "species_taxid": 2897181, "relation_to_type": "type", "validated": true, "ani": 78.6101, "matched_fragments": 346, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium proteolyticum", "strain": "strain=1Y8A", "accession": "GCA_015223105.1", "taxid": 2911683, "species_taxid": 2911683, "relation_to_type": "type", "validated": true, "ani": 78.6064, "matched_fragments": 362, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium cyclinae", "strain": "strain=KSM-R2A25", "accession": "GCA_021172145.1", "taxid": 2895947, "species_taxid": 2895947, "relation_to_type": "type", "validated": true, "ani": 78.5928, "matched_fragments": 333, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium indicum", "strain": "strain=GPTSA100-9", "accession": "GCA_000455605.1", "taxid": 312277, "species_taxid": 312277, "relation_to_type": "type", "validated": true, "ani": 78.4206, "matched_fragments": 416, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium haoranii", "strain": "strain=KCTC 23008", "accession": "GCA_009363055.1", "taxid": 683124, "species_taxid": 683124, "relation_to_type": "type", "validated": true, "ani": 78.2406, "matched_fragments": 282, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium haoranii", "strain": "strain=DSM 22807", "accession": "GCA_900142055.1", "taxid": 683124, "species_taxid": 683124, "relation_to_type": "type", "validated": true, "ani": 78.1741, "matched_fragments": 279, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium aquatile", "strain": "strain=LMG 4008", "accession": "GCA_000757385.1", "taxid": 245, "species_taxid": 245, "relation_to_type": "type", "validated": true, "ani": 77.9675, "matched_fragments": 268, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium jejuense", "strain": "strain=EC11", "accession": "GCA_006491595.2", "taxid": 1544455, "species_taxid": 1544455, "relation_to_type": "type", "validated": true, "ani": 77.7722, "matched_fragments": 312, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium sediminilitoris", "strain": "strain=YSM-43", "accession": "GCA_023008245.1", "taxid": 2024526, "species_taxid": 2024526, "relation_to_type": "type", "validated": true, "ani": 77.7573, "matched_fragments": 280, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium davisii", "strain": "strain=90-106", "accession": "GCA_019565505.1", "taxid": 2906077, "species_taxid": 2906077, "relation_to_type": "type", "validated": true, "ani": 77.3701, "matched_fragments": 182, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium soyae", "strain": "strain=SCIV07", "accession": "GCA_021245985.1", "taxid": 2903098, "species_taxid": 2903098, "relation_to_type": "type", "validated": true, "ani": 77.2717, "matched_fragments": 194, "total_fragments": 975, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011392115.1", "gtdb_species": "s__Flavobacterium sp011392115", "ani": 100.0, "matched_fragments": 973, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": "GCF_011305415.1", "gtdb_species": "s__Flavobacterium bernardetii", "ani": 84.9488, "matched_fragments": 712, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_900108955.1", "gtdb_species": "s__Flavobacterium terrigena", "ani": 84.3271, "matched_fragments": 692, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_001800945.1", "gtdb_species": "s__Flavobacterium sp001800945", "ani": 84.0282, "matched_fragments": 447, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_017985075.1", "gtdb_species": "s__Flavobacterium sp017985075", "ani": 82.2178, "matched_fragments": 506, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_004293045.1", "gtdb_species": "s__Flavobacterium sp004293045", "ani": 82.0749, "matched_fragments": 412, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_900110615.1", "gtdb_species": "s__Flavobacterium urocaniciphilum", "ani": 81.3118, "matched_fragments": 617, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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_003525665.1", "gtdb_species": "s__Flavobacterium sp003525665", "ani": 77.6461, "matched_fragments": 277, "total_fragments": 975, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "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": -0.326, "cell_length": 0.278, "doubling_h": 1.271, "growth_tmp": 24.705, "optimum_tmp": 25.047, "optimum_ph": 7.141, "genome_size": 3988255.815, "gc_content": 34.893, "coding_genes": 3154.048, "rRNA16S_genes": 5.145, "tRNA_genes": 58.611, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.347, "range_salinity": 0.333, "facultative_respiration": 0.049, "anaerobic_respiration": 0.019, "aerobic_respiration": 0.931, "mesophilic_range_tmp": 0.789, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.21, "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": [ "Flavobacterium", "difficile" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }