{ "type": "genome", "identifier": "GCF_900142355.1", "organism": "Flavobacterium johnsoniae", "title": "Flavobacterium johnsoniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900142355.1", "bioproject": "PRJNA224116", "biosample": "SAMN05444146", "wgs_master": "FRAO00000000.1", "refseq_category": "na", "taxid": "986", "species_taxid": "986", "organism_name": "Flavobacterium johnsoniae", "infraspecific_name": "strain=DSM 2064", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2698536700 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900142355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/142/355/GCF_900142355.1_IMG-taxon_2698536700_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6052484", "genome_size_ungapped": "6052439", "gc_percent": "34.000000", "replicon_count": "0", "scaffold_count": "16", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900142355.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5232", "protein_coding_gene_count": "5132", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-03", "dateModified": "2016-12-03", "datePublished": "2016-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Flavobacterium johnsoniae" ], "sample_taxid": [ "986" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.677 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)": "6052484", "Number of Sequences": "16", "Longest Sequences (bp)": "1629892", "N50 (bp)": "997149", "Gap Ratio (%)": "0.000743", "GCcontent (%)": "34.0", "Number of CDSs": "5136", "Average Protein Length": "342.5", "Coding Ratio (%)": "87.2", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Flavobacterium johnsoniae", "strain": "strain=DSM 2064", "accession": "GCA_900142355.1", "taxid": 986, "species_taxid": 986, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2008, "total_fragments": 2010, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium johnsoniae", "strain": "strain=UW101; ATCC 17061", "accession": "GCA_000016645.1", "taxid": 986, "species_taxid": 986, "relation_to_type": "type", "validated": true, "ani": 99.999, "matched_fragments": 2009, "total_fragments": 2010, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium johnsoniae", "strain": "strain=ATCC 17061", "accession": "GCA_002221975.1", "taxid": 986, "species_taxid": 986, "relation_to_type": "type", "validated": true, "ani": 99.9798, "matched_fragments": 1974, "total_fragments": 2010, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium panici", "strain": "", "accession": "GCA_903819335.1", "taxid": 2654843, "species_taxid": 2654843, "relation_to_type": "type", "validated": true, "ani": 86.1882, "matched_fragments": 1323, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium defluvii", "strain": "strain=DSM 17963", "accession": "GCA_900129555.1", "taxid": 370979, "species_taxid": 370979, "relation_to_type": "type", "validated": true, "ani": 86.1172, "matched_fragments": 1269, "total_fragments": 2010, "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": 86.0704, "matched_fragments": 1210, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium endoglycinae", "strain": "strain=BB8", "accession": "GCA_017352115.1", "taxid": 2816357, "species_taxid": 2816357, "relation_to_type": "type", "validated": true, "ani": 84.4883, "matched_fragments": 1341, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium nitrogenifigens", "strain": "strain=DSM 29982", "accession": "GCA_900182675.1", "taxid": 1617283, "species_taxid": 1617283, "relation_to_type": "type", "validated": true, "ani": 84.3315, "matched_fragments": 1203, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium nitrogenifigens", "strain": "strain=NXU-44", "accession": "GCA_003254565.1", "taxid": 1617283, "species_taxid": 1617283, "relation_to_type": "type", "validated": true, "ani": 84.2908, "matched_fragments": 1188, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium tyrosinilyticum", "strain": "strain=KCTC 42726", "accession": "GCA_023656565.1", "taxid": 1658740, "species_taxid": 1658740, "relation_to_type": "type", "validated": true, "ani": 84.2358, "matched_fragments": 1244, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium anhuiense", "strain": "strain=CGMCC 1.6859", "accession": "GCA_900101855.1", "taxid": 459526, "species_taxid": 459526, "relation_to_type": "suspected-type", "validated": true, "ani": 83.9651, "matched_fragments": 1216, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium phragmitis", "strain": "strain=CGMCC 1.10370", "accession": "GCA_900112575.1", "taxid": 739143, "species_taxid": 739143, "relation_to_type": "type", "validated": true, "ani": 83.896, "matched_fragments": 1261, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium panacis", "strain": "strain=DCY106", "accession": "GCA_024649945.1", "taxid": 2962567, "species_taxid": 2962567, "relation_to_type": "type", "validated": true, "ani": 83.6903, "matched_fragments": 1213, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium zhairuonense", "strain": "strain=A5.7", "accession": "GCA_004352915.1", "taxid": 2493631, "species_taxid": 2493631, "relation_to_type": "type", "validated": true, "ani": 83.5883, "matched_fragments": 1129, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium denitrificans", "strain": "strain=DSM 15936", "accession": "GCA_000425445.1", "taxid": 281361, "species_taxid": 281361, "relation_to_type": "type", "validated": true, "ani": 83.5523, "matched_fragments": 1064, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium amniphilum", "strain": "strain=KYPY10", "accession": "GCA_023634845.1", "taxid": 1834035, "species_taxid": 1834035, "relation_to_type": "type", "validated": true, "ani": 77.3078, "matched_fragments": 189, "total_fragments": 2010, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000016645.1", "gtdb_species": "s__Flavobacterium johnsoniae", "ani": 99.999, "matched_fragments": 2009, "total_fragments": 2010, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.86", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_900129555.1", "gtdb_species": "s__Flavobacterium defluvii", "ani": 86.1081, "matched_fragments": 1270, "total_fragments": 2010, "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_002210235.1", "gtdb_species": "s__Flavobacterium sp002210235", "ani": 86.0665, "matched_fragments": 1340, "total_fragments": 2010, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900129795.1", "gtdb_species": "s__Flavobacterium sp900129795", "ani": 86.0318, "matched_fragments": 1296, "total_fragments": 2010, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002482975.1", "gtdb_species": "s__Flavobacterium sp002482975", "ani": 85.8832, "matched_fragments": 1296, "total_fragments": 2010, "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_001428525.1", "gtdb_species": "s__Flavobacterium sp001428525", "ani": 85.882, "matched_fragments": 1323, "total_fragments": 2010, "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_001429765.1", "gtdb_species": "s__Flavobacterium sp001429765", "ani": 85.0026, "matched_fragments": 1242, "total_fragments": 2010, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013388355.1", "gtdb_species": "s__Flavobacterium sp013388355", "ani": 84.6711, "matched_fragments": 885, "total_fragments": 2010, "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_003254585.1", "gtdb_species": "s__Flavobacterium sharifuzzamanii", "ani": 84.352, "matched_fragments": 1220, "total_fragments": 2010, "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_002303885.1", "gtdb_species": "s__Flavobacterium sp002303885", "ani": 84.35, "matched_fragments": 1236, "total_fragments": 2010, "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_003254565.1", "gtdb_species": "s__Flavobacterium nitrogenifigens", "ani": 84.3025, "matched_fragments": 1187, "total_fragments": 2010, "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": 3, "status": "-" }, { "accession": "GCF_016735615.1", "gtdb_species": "s__Flavobacterium sp016735615", "ani": 84.0999, "matched_fragments": 1204, "total_fragments": 2010, "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_003312915.1", "gtdb_species": "s__Flavobacterium sp003312915", "ani": 84.0067, "matched_fragments": 1140, "total_fragments": 2010, "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_900101855.1", "gtdb_species": "s__Flavobacterium anhuiense", "ani": 83.9314, "matched_fragments": 1221, "total_fragments": 2010, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "97.43", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900112575.1", "gtdb_species": "s__Flavobacterium phragmitis", "ani": 83.8852, "matched_fragments": 1262, "total_fragments": 2010, "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_014207905.1", "gtdb_species": "s__Flavobacterium notoginsengisoli", "ani": 83.788, "matched_fragments": 1207, "total_fragments": 2010, "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_009711135.1", "gtdb_species": "s__Flavobacterium sp009711135", "ani": 83.78, "matched_fragments": 1136, "total_fragments": 2010, "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_004352915.1", "gtdb_species": "s__Flavobacterium zhairuonense", "ani": 83.5838, "matched_fragments": 1130, "total_fragments": 2010, "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_000425445.1", "gtdb_species": "s__Flavobacterium denitrificans", "ani": 83.5462, "matched_fragments": 1065, "total_fragments": 2010, "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_004362055.1", "gtdb_species": "s__Flavobacterium sp004362055", "ani": 83.5281, "matched_fragments": 1098, "total_fragments": 2010, "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_015182285.1", "gtdb_species": "s__Flavobacterium sp015182285", "ani": 82.9036, "matched_fragments": 1227, "total_fragments": 2010, "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_017833855.1", "gtdb_species": "s__Flavobacterium sp017833855", "ani": 82.8539, "matched_fragments": 1139, "total_fragments": 2010, "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": -0.523, "cell_length": 0.176, "doubling_h": 1.271, "growth_tmp": 27.667, "optimum_tmp": 26.667, "optimum_ph": 7.141, "genome_size": 5675748.0, "gc_content": 34.167, "coding_genes": 4645.333, "rRNA16S_genes": 5.5, "tRNA_genes": 63.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 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", "johnsoniae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }