{ "type": "genome", "identifier": "GCF_016623605.1", "organism": "Kingella bonacorsii", "title": "Kingella bonacorsii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "IHU - MI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016623605.1", "bioproject": "PRJNA224116", "biosample": "SAMN17082536", "wgs_master": "JAEHNZ000000000.1", "refseq_category": "reference genome", "taxid": "2796361", "species_taxid": "2796361", "organism_name": "Kingella bonacorsii", "infraspecific_name": "strain=Marseille-Q4569", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/01/05", "asm_name": "ASM1662360v1", "asm_submitter": "IHU - MI", "gbrs_paired_asm": "GCA_016623605.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/623/605/GCF_016623605.1_ASM1662360v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2502986", "genome_size_ungapped": "2502976", "gc_percent": "54.000000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016623605.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "2754", "protein_coding_gene_count": "2636", "non_coding_gene_count": "71", "pubmed_id": "33669894" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-01-05", "dateModified": "2021-01-05", "datePublished": "2021-01-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Kingella bonacorsii" ], "sample_taxid": [ "2796361" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Marseille" ], "sample_host_location_id": [], "data_size": "0.686 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 96.12, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2502986", "Number of Sequences": "9", "Longest Sequences (bp)": "917951", "N50 (bp)": "749790", "Gap Ratio (%)": "0.000719", "GCcontent (%)": "54.0", "Number of CDSs": "2489", "Average Protein Length": "276.0", "Coding Ratio (%)": "82.3", "Number of rRNAs": "12", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Kingella bonacorsii", "strain": "strain=Marseille-Q4569", "accession": "GCA_016623605.1", "taxid": 2796361, "species_taxid": 2796361, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 825, "total_fragments": 829, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Kingella oralis", "strain": "strain=DSM 18271", "accession": "GCA_014054985.1", "taxid": 505, "species_taxid": 505, "relation_to_type": "type", "validated": true, "ani": 96.4452, "matched_fragments": 729, "total_fragments": 829, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Kingella oralis", "strain": "strain=ATCC 51147", "accession": "GCA_000160435.1", "taxid": 505, "species_taxid": 505, "relation_to_type": "type", "validated": true, "ani": 96.44, "matched_fragments": 723, "total_fragments": 829, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Neisseria bacilliformis", "strain": "strain=DSM 23338", "accession": "GCA_014055025.1", "taxid": 267212, "species_taxid": 267212, "relation_to_type": "type", "validated": true, "ani": 79.9026, "matched_fragments": 321, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria bacilliformis", "strain": "strain=ATCC BAA-1200", "accession": "GCA_000194925.1", "taxid": 267212, "species_taxid": 267212, "relation_to_type": "type", "validated": true, "ani": 79.776, "matched_fragments": 304, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella denitrificans", "strain": "strain=FDAARGOS_1060", "accession": "GCA_016127355.1", "taxid": 502, "species_taxid": 502, "relation_to_type": "type", "validated": true, "ani": 79.5054, "matched_fragments": 345, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella denitrificans", "strain": "strain=ATCC 33394", "accession": "GCA_000190695.1", "taxid": 502, "species_taxid": 502, "relation_to_type": "type", "validated": true, "ani": 79.2673, "matched_fragments": 333, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella potus", "strain": "strain=NCTC13336", "accession": "GCA_900451175.1", "taxid": 265175, "species_taxid": 265175, "relation_to_type": "type", "validated": true, "ani": 78.9142, "matched_fragments": 267, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eikenella longinqua", "strain": "strain=NML02-A-017", "accession": "GCA_001648355.1", "taxid": 1795827, "species_taxid": 1795827, "relation_to_type": "type", "validated": true, "ani": 78.4214, "matched_fragments": 247, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kingella kingae", "strain": "strain=4177/66", "accession": "GCA_022871005.1", "taxid": 504, "species_taxid": 504, "relation_to_type": "type", "validated": true, "ani": 78.3749, "matched_fragments": 245, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neisseria dumasiana", "strain": "strain=LMG 30012", "accession": "GCA_022870885.1", "taxid": 1931275, "species_taxid": 1931275, "relation_to_type": "type", "validated": true, "ani": 78.1377, "matched_fragments": 217, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alysiella crassa", "strain": "strain=S6", "accession": "GCA_022871045.1", "taxid": 153491, "species_taxid": 153491, "relation_to_type": "type", "validated": true, "ani": 78.0406, "matched_fragments": 292, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Uruburuella suis", "strain": "strain=1258/02", "accession": "GCA_022870845.1", "taxid": 252130, "species_taxid": 252130, "relation_to_type": "type", "validated": true, "ani": 77.8841, "matched_fragments": 256, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alysiella crassa", "strain": "strain=DSM 2578", "accession": "GCA_000745955.1", "taxid": 153491, "species_taxid": 153491, "relation_to_type": "type", "validated": true, "ani": 77.7751, "matched_fragments": 270, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Uruburuella testudinis", "strain": "strain=CCUG 63373m", "accession": "GCA_022870865.1", "taxid": 1282863, "species_taxid": 1282863, "relation_to_type": "type", "validated": true, "ani": 77.6176, "matched_fragments": 217, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Uruburuella suis", "strain": "strain=DSM 17474", "accession": "GCA_004341385.1", "taxid": 252130, "species_taxid": 252130, "relation_to_type": "type", "validated": true, "ani": 77.5942, "matched_fragments": 241, "total_fragments": 829, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 96.12, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014054985.1", "gtdb_species": "s__Kingella_B oralis", "ani": 96.4582, "matched_fragments": 732, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_905373195.1", "gtdb_species": "s__Kingella_B oralis_A", "ani": 91.4674, "matched_fragments": 345, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B", "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_014055025.1", "gtdb_species": "s__Neisseria bacilliformis", "ani": 79.8693, "matched_fragments": 321, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "96.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000190695.1", "gtdb_species": "s__Kingella_A denitrificans", "ani": 79.2673, "matched_fragments": 333, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003990355.1", "gtdb_species": "s__Eikenella corrodens_B", "ani": 79.2663, "matched_fragments": 246, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "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_900187105.1", "gtdb_species": "s__Eikenella corrodens", "ani": 79.0819, "matched_fragments": 223, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "95.30", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_002237445.1", "gtdb_species": "s__Neisseria sp002237445", "ani": 78.9054, "matched_fragments": 258, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900451175.1", "gtdb_species": "s__Neisseria potus", "ani": 78.8892, "matched_fragments": 267, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "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_001648475.1", "gtdb_species": "s__Eikenella halliae", "ani": 78.8775, "matched_fragments": 240, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "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_900636765.1", "gtdb_species": "s__Neisseria canis", "ani": 78.7317, "matched_fragments": 176, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "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": "GCF_005886145.1", "gtdb_species": "s__Neisseria sp000090875", "ani": 78.5083, "matched_fragments": 244, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "97.41", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001648355.1", "gtdb_species": "s__Eikenella longinqua", "ani": 78.4272, "matched_fragments": 247, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "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_016025525.2", "gtdb_species": "s__Eikenella sp016025525", "ani": 78.3829, "matched_fragments": 245, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella", "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_002216145.1", "gtdb_species": "s__Neisseria chenwenguii", "ani": 78.2755, "matched_fragments": 248, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "99.73", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014054525.1", "gtdb_species": "s__Alysiella filiformis", "ani": 78.1819, "matched_fragments": 290, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella", "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": "GCF_008807015.1", "gtdb_species": "s__Neisseria zalophi", "ani": 78.073, "matched_fragments": 96, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "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_000751855.1", "gtdb_species": "s__Kingella negevensis", "ani": 77.9747, "matched_fragments": 280, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002108505.1", "gtdb_species": "s__Neisseria dumasiana", "ani": 77.8353, "matched_fragments": 209, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.54", "min_intra_species_ani": "97.26", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000745955.1", "gtdb_species": "s__Alysiella crassa", "ani": 77.7704, "matched_fragments": 272, "total_fragments": 829, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 35.5, "optimum_tmp": 35.0, "optimum_ph": null, "genome_size": 2189783.662, "gc_content": 50.425, "coding_genes": 2114.0, "rRNA16S_genes": 4.0, "tRNA_genes": 54.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.5, "range_salinity": null, "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": 0.666, "coccus_cell_shape": 0.333, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Kingella", "bonacorsii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }