{ "type": "genome", "identifier": "GCF_900142685.1", "organism": "Flavobacterium chilense", "title": "Flavobacterium chilense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900142685.1", "bioproject": "PRJNA224116", "biosample": "SAMN05444484", "wgs_master": "FRBT00000000.1", "refseq_category": "reference genome", "taxid": "946677", "species_taxid": "946677", "organism_name": "Flavobacterium chilense", "infraspecific_name": "strain=DSM 24724", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2700988709 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900142685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/142/685/GCF_900142685.1_IMG-taxon_2700988709_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": "6113833", "genome_size_ungapped": "6113833", "gc_percent": "33.500000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900142685.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "5179", "protein_coding_gene_count": "5077", "non_coding_gene_count": "75", "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 chilense" ], "sample_taxid": [ "946677" ], "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": "1.696 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)": "6113833", "Number of Sequences": "28", "Longest Sequences (bp)": "1918638", "N50 (bp)": "507764", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "33.7", "Number of CDSs": "5104", "Average Protein Length": "347.2", "Coding Ratio (%)": "87.0", "Number of rRNAs": "2", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Flavobacterium chilense", "strain": "strain=DSM 24724", "accession": "GCA_900142685.1", "taxid": 946677, "species_taxid": 946677, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2021, "total_fragments": 2024, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium chilense", "strain": "strain=LMG 26360", "accession": "GCA_001602525.1", "taxid": 946677, "species_taxid": 946677, "relation_to_type": "type", "validated": true, "ani": 99.9957, "matched_fragments": 1958, "total_fragments": 2024, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium bizetiae", "strain": "strain=CIP 105534", "accession": "GCA_904425415.1", "taxid": 2704140, "species_taxid": 2704140, "relation_to_type": "type", "validated": true, "ani": 84.7351, "matched_fragments": 1249, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium bizetiae", "strain": "strain=CIP 105534", "accession": "GCA_902804475.1", "taxid": 2704140, "species_taxid": 2704140, "relation_to_type": "type", "validated": true, "ani": 84.7348, "matched_fragments": 1221, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium aquidurense", "strain": "strain=DSM 18293", "accession": "GCA_002217195.1", "taxid": 362413, "species_taxid": 362413, "relation_to_type": "type", "validated": true, "ani": 84.1852, "matched_fragments": 1227, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium piscis", "strain": "strain=CCUG 60099", "accession": "GCA_002222045.1", "taxid": 1114874, "species_taxid": 1114874, "relation_to_type": "type", "validated": true, "ani": 84.1731, "matched_fragments": 1175, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium piscis", "strain": "strain=CCUG 60099", "accession": "GCA_001686925.1", "taxid": 1114874, "species_taxid": 1114874, "relation_to_type": "type", "validated": true, "ani": 84.1438, "matched_fragments": 1206, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium psychroterrae", "strain": "strain=CCM 8827", "accession": "GCA_018380615.1", "taxid": 2133767, "species_taxid": 2133767, "relation_to_type": "type", "validated": true, "ani": 84.12, "matched_fragments": 1274, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium panici", "strain": "", "accession": "GCA_903819335.1", "taxid": 2654843, "species_taxid": 2654843, "relation_to_type": "type", "validated": true, "ani": 83.8894, "matched_fragments": 1158, "total_fragments": 2024, "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": 83.7193, "matched_fragments": 1106, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium plurextorum", "strain": "strain=CCUG 60112", "accession": "GCA_002217395.1", "taxid": 1114867, "species_taxid": 1114867, "relation_to_type": "type", "validated": true, "ani": 83.6527, "matched_fragments": 1097, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium oncorhynchi", "strain": "strain=CCUG 59446", "accession": "GCA_002217355.1", "taxid": 728056, "species_taxid": 728056, "relation_to_type": "type", "validated": true, "ani": 83.5477, "matched_fragments": 1113, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium collinsii", "strain": "", "accession": "GCA_902804485.1", "taxid": 1114861, "species_taxid": 1114861, "relation_to_type": "type", "validated": true, "ani": 83.133, "matched_fragments": 1144, "total_fragments": 2024, "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": 82.5805, "matched_fragments": 1093, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium quisquiliarum", "strain": "strain=EA-12", "accession": "GCA_019308285.1", "taxid": 1834436, "species_taxid": 1834436, "relation_to_type": "type", "validated": true, "ani": 82.5616, "matched_fragments": 1120, "total_fragments": 2024, "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": 82.3126, "matched_fragments": 1103, "total_fragments": 2024, "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": 82.2979, "matched_fragments": 1090, "total_fragments": 2024, "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": 82.1181, "matched_fragments": 1110, "total_fragments": 2024, "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": 76.7938, "matched_fragments": 239, "total_fragments": 2024, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001602525.1", "gtdb_species": "s__Flavobacterium chilense", "ani": 99.9829, "matched_fragments": 1959, "total_fragments": 2024, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "96.61", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_001422725.1", "gtdb_species": "s__Flavobacterium sp001422725", "ani": 84.607, "matched_fragments": 1272, "total_fragments": 2024, "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", 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"status": "-" }, { "accession": "GCA_900129595.1", "gtdb_species": "s__Flavobacterium frigidimaris", "ani": 84.2098, "matched_fragments": 1230, "total_fragments": 2024, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002754195.1", "gtdb_species": "s__Flavobacterium sp002754195", "ani": 84.0479, "matched_fragments": 1237, "total_fragments": 2024, "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_004339525.1", "gtdb_species": "s__Flavobacterium sp004339525", "ani": 83.9673, "matched_fragments": 1243, "total_fragments": 2024, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006438875.1", "gtdb_species": "s__Flavobacterium pectinovorum_A", "ani": 83.9067, "matched_fragments": 1250, "total_fragments": 2024, "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_003217415.1", "gtdb_species": "s__Flavobacterium sp003217415", "ani": 83.8154, "matched_fragments": 1214, "total_fragments": 2024, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002210235.1", "gtdb_species": "s__Flavobacterium sp002210235", "ani": 83.7895, "matched_fragments": 1173, "total_fragments": 2024, "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": 83.7726, "matched_fragments": 1167, "total_fragments": 2024, "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": 83.6849, "matched_fragments": 1178, "total_fragments": 2024, "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_002217395.1", "gtdb_species": 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"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_900112575.1", "gtdb_species": "s__Flavobacterium phragmitis", "ani": 82.2906, "matched_fragments": 1091, "total_fragments": 2024, "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": -0.071, "cell_length": 0.352, "doubling_h": 1.271, "growth_tmp": 28.0, "optimum_tmp": 27.0, "optimum_ph": 7.5, "genome_size": 6019171.5, "gc_content": 34.893, "coding_genes": 3154.048, "rRNA16S_genes": 5.145, "tRNA_genes": 58.611, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "chilense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }