{ "type": "genome", "identifier": "GCF_002807015.1", "organism": "Avrilella dinanensis", "title": "Avrilella dinanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CHU de Rennes", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002807015.1", "bioproject": "PRJNA224116", "biosample": "SAMN07198457", "wgs_master": "NIPO00000000.1", "refseq_category": "reference genome", "taxid": "2008672", "species_taxid": "2008672", "organism_name": "Avrilella dinanensis", "infraspecific_name": "strain=UR159", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/04", "asm_name": "ASM280701v1", "asm_submitter": "CHU de Rennes", "gbrs_paired_asm": "GCA_002807015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/807/015/GCF_002807015.1_ASM280701v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2331799", "genome_size_ungapped": "2331799", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002807015.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "2268", "protein_coding_gene_count": "2186", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-12-04", "dateModified": "2017-12-04", "datePublished": "2017-12-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Avrilella dinanensis" ], "sample_taxid": [ "2008672" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "Bloodstream infection" ], "sample_host_disease_id": [], "sample_host_location": [ "France: Dinan" ], "sample_host_location_id": [], "data_size": "0.654 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 93.75, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2331799", "Number of Sequences": "3", "Longest Sequences (bp)": "2273643", "N50 (bp)": "2273643", "Gap Ratio (%)": "0.000772", "GCcontent (%)": "37.6", "Number of CDSs": "2189", "Average Protein Length": "321.1", "Coding Ratio (%)": "90.4", "Number of rRNAs": "7", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Avrilella dinanensis", "strain": "strain=UR159", "accession": "GCA_002807015.1", "taxid": 2008672, "species_taxid": 2008672, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 775, "total_fragments": 775, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Flavobacterium viscosum", "strain": "strain=YIM 102796", "accession": "GCA_003858535.1", "taxid": 2488729, "species_taxid": 2488729, "relation_to_type": "type", "validated": true, "ani": 78.1812, "matched_fragments": 127, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides phaeus", "strain": "strain=DSM 23313", "accession": "GCA_900099675.1", "taxid": 702745, "species_taxid": 702745, "relation_to_type": "type", "validated": true, "ani": 77.9769, "matched_fragments": 50, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium baculatum", "strain": "strain=SNL9", "accession": "GCA_008629655.1", "taxid": 2608000, "species_taxid": 2608000, "relation_to_type": "type", "validated": true, "ani": 77.4476, "matched_fragments": 108, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides odoratus", "strain": "strain=FDAARGOS_1131", "accession": "GCA_016726985.1", "taxid": 256, "species_taxid": 256, "relation_to_type": "type", "validated": true, "ani": 77.1987, "matched_fragments": 57, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium ummariense", "strain": "strain=DS-12", "accession": "GCA_900115115.1", "taxid": 913024, "species_taxid": 913024, "relation_to_type": "type", "validated": true, "ani": 77.1872, "matched_fragments": 144, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Myroides odoratus", "strain": "strain=NCTC11036", "accession": "GCA_900453865.1", "taxid": 256, "species_taxid": 256, "relation_to_type": "type", "validated": true, "ani": 77.1815, "matched_fragments": 58, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium filum", "strain": "strain=DSM 17961", "accession": "GCA_000425465.1", "taxid": 370974, "species_taxid": 370974, "relation_to_type": "type", "validated": true, "ani": 77.1613, "matched_fragments": 67, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium lindanitolerans", "strain": "strain=DSM 21886", "accession": "GCA_003663835.1", "taxid": 428988, "species_taxid": 428988, "relation_to_type": "type", "validated": true, "ani": 77.1303, "matched_fragments": 67, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium cauense", "strain": "strain=CGMCC 1.7270", "accession": "GCA_007830385.1", "taxid": 510946, "species_taxid": 510946, "relation_to_type": "type", "validated": true, "ani": 77.1196, "matched_fragments": 84, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium lindanitolerans", "strain": "strain=IP-10", "accession": "GCA_002846575.1", "taxid": 428988, "species_taxid": 428988, "relation_to_type": "type", "validated": true, "ani": 77.0653, "matched_fragments": 67, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium enshiense", "strain": "strain=DK69", "accession": "GCA_000498495.1", "taxid": 1341165, "species_taxid": 1341165, "relation_to_type": "type", "validated": true, "ani": 77.0266, "matched_fragments": 70, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium microcysteis", "strain": "strain=MaA-Y11", "accession": "GCA_006385255.1", "taxid": 2596891, "species_taxid": 2596891, "relation_to_type": "type", "validated": true, "ani": 76.9082, "matched_fragments": 63, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium swingsii", "strain": "strain=DSM 21789", "accession": "GCA_900111965.1", "taxid": 498292, "species_taxid": 498292, "relation_to_type": "type", "validated": true, "ani": 76.8109, "matched_fragments": 57, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium enshiense", "strain": "strain=DK69", "accession": "GCA_000769895.1", "taxid": 1341165, "species_taxid": 1341165, "relation_to_type": "type", "validated": true, "ani": 76.8095, "matched_fragments": 71, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium luteum", "strain": "strain=NBRC 112527", "accession": "GCA_008806775.1", "taxid": 2026654, "species_taxid": 2026654, "relation_to_type": "type", "validated": true, "ani": 76.4986, "matched_fragments": 50, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavobacterium sharifuzzamanii", "strain": "strain=A7.6", "accession": "GCA_003254585.1", "taxid": 2211133, "species_taxid": 2211133, "relation_to_type": "type", "validated": true, "ani": 76.3725, "matched_fragments": 57, "total_fragments": 775, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 93.75, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002807015.1", "gtdb_species": "s__Flavobacterium dinanensis", "ani": 100.0, "matched_fragments": 775, "total_fragments": 775, "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_900108395.1", "gtdb_species": "s__Flavobacterium marinum", "ani": 79.0251, "matched_fragments": 161, "total_fragments": 775, "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_004151275.1", "gtdb_species": "s__Flavobacterium sp004151275", "ani": 78.7146, "matched_fragments": 163, "total_fragments": 775, "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_003858535.1", "gtdb_species": "s__Flavobacterium viscosum", "ani": 78.1753, "matched_fragments": 126, "total_fragments": 775, "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_013874595.1", "gtdb_species": "s__Flavobacterium sp013874595", "ani": 78.0989, "matched_fragments": 91, "total_fragments": 775, "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": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900099675.1", "gtdb_species": "s__Flavobacterium phaeum", "ani": 77.9769, "matched_fragments": 50, "total_fragments": 775, "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_008629655.1", "gtdb_species": "s__Flavobacterium baculatum", "ani": 77.4476, "matched_fragments": 108, "total_fragments": 775, "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_009799805.1", "gtdb_species": "s__Flavobacterium phaeum_A", "ani": 77.4225, "matched_fragments": 57, "total_fragments": 775, "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_000243275.1", "gtdb_species": "s__Flavobacterium odoratum", "ani": 77.208, "matched_fragments": 56, "total_fragments": 775, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.25", "min_intra_species_ani": "95.68", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001549985.1", "gtdb_species": "s__Flavobacterium odoratum_A", "ani": 77.1939, "matched_fragments": 53, "total_fragments": 775, "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_900115115.1", "gtdb_species": "s__Flavobacterium ummariense", "ani": 77.1766, "matched_fragments": 143, "total_fragments": 775, "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_000425465.1", "gtdb_species": "s__Flavobacterium filum", "ani": 77.1613, "matched_fragments": 67, "total_fragments": 775, "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_002846575.1", "gtdb_species": "s__Flavobacterium lindanitolerans", "ani": 77.0926, "matched_fragments": 68, "total_fragments": 775, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.86", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_000498495.1", "gtdb_species": "s__Flavobacterium enshiense", "ani": 77.0266, "matched_fragments": 70, "total_fragments": 775, "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": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006385255.1", "gtdb_species": "s__Flavobacterium microcysteis", "ani": 76.9082, "matched_fragments": 63, "total_fragments": 775, "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_900111965.1", "gtdb_species": "s__Flavobacterium swingsii", "ani": 76.8109, "matched_fragments": 57, "total_fragments": 775, "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_014145635.1", "gtdb_species": "s__Flavobacterium sp014145635", "ani": 76.5274, "matched_fragments": 64, "total_fragments": 775, "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_008806775.1", "gtdb_species": "s__Flavobacterium luteum", "ani": 76.4986, "matched_fragments": 50, "total_fragments": 775, "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": 76.3725, "matched_fragments": 57, "total_fragments": 775, "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": 76.3142, "matched_fragments": 63, "total_fragments": 775, "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Avrilella", "dinanensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }