{ "type": "genome", "identifier": "GCF_013401995.1", "organism": "Flavobacterium agri", "title": "Flavobacterium agri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MRCEN World Data Centre for Microoganisms(WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013401995.1", "bioproject": "PRJNA224116", "biosample": "SAMN15455295", "wgs_master": "JACBJI000000000.1", "refseq_category": "na", "taxid": "2743471", "species_taxid": "2743471", "organism_name": "Flavobacterium agri", "infraspecific_name": "strain=MAH-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/11", "asm_name": "ASM1340199v1", "asm_submitter": "WFCC-MRCEN World Data Centre for Microoganisms(WDCM)", "gbrs_paired_asm": "GCA_013401995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/401/995/GCF_013401995.1_ASM1340199v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3976830", "genome_size_ungapped": "3975600", "gc_percent": "47.000000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013401995.1-RS_2024_08_22", "annotation_date": "2024-08-22", "total_gene_count": "3599", "protein_coding_gene_count": "3528", "non_coding_gene_count": "46", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-11", "dateModified": "2020-07-11", "datePublished": "2020-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Flavobacterium agri" ], "sample_taxid": [ "2743471" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.120 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.62, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3976830", "Number of Sequences": "39", "Longest Sequences (bp)": "864336", "N50 (bp)": "609468", "Gap Ratio (%)": "0.030929", "GCcontent (%)": "47.1", "Number of CDSs": "3511", "Average Protein Length": "334.0", "Coding Ratio (%)": "88.5", "Number of rRNAs": "3", "Number of tRNAs": "38", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Flavobacterium agri", "strain": "strain=MAH-1", "accession": "GCA_013401995.1", "taxid": 2743471, "species_taxid": 2743471, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1306, "total_fragments": 1306, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium agri", "strain": "strain=MAH-1", "accession": "GCA_013366395.1", "taxid": 2743471, "species_taxid": 2743471, "relation_to_type": "type", "validated": true, "ani": 99.9959, "matched_fragments": 1292, "total_fragments": 1306, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium silvaticum", "strain": "strain=SE-s28", "accession": "GCA_012911565.1", "taxid": 1852020, "species_taxid": 1852020, "relation_to_type": "type", "validated": true, "ani": 77.9734, "matched_fragments": 324, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium caeni", "strain": "strain=CGMCC 1.7031", "accession": "GCA_900101895.1", "taxid": 490189, "species_taxid": 490189, "relation_to_type": "type", "validated": true, "ani": 77.555, "matched_fragments": 303, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium noncentrifugens", "strain": "strain=CGMCC 1.10076", "accession": "GCA_900100375.1", "taxid": 1128970, "species_taxid": 1128970, "relation_to_type": "type", "validated": true, "ani": 77.0554, "matched_fragments": 203, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium noncentrifugens", "strain": "strain=NBRC 108844", "accession": "GCA_007992475.1", "taxid": 1128970, "species_taxid": 1128970, "relation_to_type": "type", "validated": true, "ani": 77.0234, "matched_fragments": 208, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium lotistagni", "strain": "strain=CYK-4", "accession": "GCA_011392125.1", "taxid": 2709660, "species_taxid": 2709660, "relation_to_type": "type", "validated": true, "ani": 76.898, "matched_fragments": 148, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium suncheonense", "strain": "strain=DSM 17707", "accession": "GCA_000430025.1", "taxid": 350894, "species_taxid": 350894, "relation_to_type": "type", "validated": true, "ani": 76.857, "matched_fragments": 109, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium suncheonense", "strain": "strain=GH29-5", "accession": "GCA_000769835.1", "taxid": 350894, "species_taxid": 350894, "relation_to_type": "type", "validated": true, "ani": 76.8483, "matched_fragments": 107, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium alvei", "strain": "strain=HR-AY", "accession": "GCA_002920895.1", "taxid": 2080416, "species_taxid": 2080416, "relation_to_type": "type", "validated": true, "ani": 76.7113, "matched_fragments": 52, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium palustre", "strain": "strain=CGMCC 1.12811", "accession": "GCA_014639535.1", "taxid": 1476463, "species_taxid": 1476463, "relation_to_type": "type", "validated": true, "ani": 76.7104, "matched_fragments": 62, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium magnum", "strain": "strain=HYN0048", "accession": "GCA_003055625.1", "taxid": 2162713, "species_taxid": 2162713, "relation_to_type": "type", "validated": true, "ani": 76.6176, "matched_fragments": 135, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium daemonense", "strain": "strain=JCM 19455", "accession": "GCA_007341385.1", "taxid": 1393049, "species_taxid": 1393049, "relation_to_type": "type", "validated": true, "ani": 76.5012, "matched_fragments": 60, "total_fragments": 1306, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.62, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013401995.1", "gtdb_species": "s__Flavobacterium agri", "ani": 100.0, "matched_fragments": 1306, "total_fragments": 1306, "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": "conclusive" }, { "accession": "GCA_004295795.1", "gtdb_species": "s__Flavobacterium sp004295795", "ani": 80.3095, "matched_fragments": 773, "total_fragments": 1306, "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_014748335.1", "gtdb_species": "s__Flavobacterium sp014748335", "ani": 79.8456, "matched_fragments": 693, "total_fragments": 1306, "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_004211145.1", "gtdb_species": "s__Flavobacterium sp004211145", "ani": 79.7045, "matched_fragments": 644, "total_fragments": 1306, "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_012911565.1", "gtdb_species": "s__Flavobacterium sp012911565", "ani": 77.9459, "matched_fragments": 329, "total_fragments": 1306, "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_900101895.1", "gtdb_species": "s__Flavobacterium caeni", "ani": 77.5531, "matched_fragments": 304, "total_fragments": 1306, "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_000430025.1", "gtdb_species": "s__Flavobacterium suncheonense", "ani": 76.857, "matched_fragments": 109, "total_fragments": 1306, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002483285.1", "gtdb_species": "s__Flavobacterium sp002483285", "ani": 76.7284, "matched_fragments": 216, "total_fragments": 1306, "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_015234525.1", "gtdb_species": "s__Flavobacterium sp015234525", "ani": 76.6607, "matched_fragments": 94, "total_fragments": 1306, "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", "agri" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }