{ "type": "genome", "identifier": "GCF_004296575.1", "organism": "Dyella amyloliquefaciens", "title": "Dyella amyloliquefaciens", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SUN YAT-SEN UNIVERSITY", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004296575.1", "bioproject": "PRJNA224116", "biosample": "SAMN10712956", "wgs_master": "SAYT00000000.1", "refseq_category": "reference genome", "taxid": "1770545", "species_taxid": "1770545", "organism_name": "Dyella amyloliquefaciens", "infraspecific_name": "strain=DHC06", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/25", "asm_name": "ASM429657v1", "asm_submitter": "SUN YAT-SEN UNIVERSITY", "gbrs_paired_asm": "GCA_004296575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/296/575/GCF_004296575.1_ASM429657v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4834900", "genome_size_ungapped": "4834900", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004296575.1-RS_2024_05_12", "annotation_date": "2024-05-12", "total_gene_count": "4212", "protein_coding_gene_count": "4142", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-25", "dateModified": "2019-02-25", "datePublished": "2019-02-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Dyella amyloliquefaciens" ], "sample_taxid": [ "1770545" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Guangdong Province, Dinghushan Biosphere Reserve" ], "sample_host_location_id": [], "data_size": "1.336 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)": "4834900", "Number of Sequences": "17", "Longest Sequences (bp)": "1119972", "N50 (bp)": "689779", "Gap Ratio (%)": "0.000062", "GCcontent (%)": "64.6", "Number of CDSs": "4238", "Average Protein Length": "334.7", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Dyella amyloliquefaciens", "strain": "strain=DHC06", "accession": "GCA_004296575.1", "taxid": 1770545, "species_taxid": 1770545, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1602, "total_fragments": 1603, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Dyella solisilvae", "strain": "strain=DHG54", "accession": "GCA_003351225.1", "taxid": 1920168, "species_taxid": 1920168, "relation_to_type": "type", "validated": true, "ani": 84.7578, "matched_fragments": 1058, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella telluris", "strain": "strain=G9", "accession": "GCA_014297575.1", "taxid": 2763498, "species_taxid": 2763498, "relation_to_type": "type", "validated": true, "ani": 84.1877, "matched_fragments": 1092, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella kyungheensis", "strain": "strain=THG-B117", "accession": "GCA_016905005.1", "taxid": 1242174, "species_taxid": 1242174, "relation_to_type": "type", "validated": true, "ani": 84.0596, "matched_fragments": 1032, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella japonica", "strain": "strain=DSM 16301", "accession": "GCA_001010355.1", "taxid": 231455, "species_taxid": 231455, "relation_to_type": "type", "validated": true, "ani": 83.8471, "matched_fragments": 873, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=LMG 19981", "accession": "GCA_006352285.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 82.1679, "matched_fragments": 720, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frateuria flava", "strain": "strain=MAH-13", "accession": "GCA_017837635.1", "taxid": 2821489, "species_taxid": 2821489, "relation_to_type": "type", "validated": true, "ani": 81.2511, "matched_fragments": 645, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella acidiphila", "strain": "strain=7MK23", "accession": "GCA_014863405.1", "taxid": 2775866, "species_taxid": 2775866, "relation_to_type": "type", "validated": true, "ani": 80.6988, "matched_fragments": 709, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tahibacter caeni", "strain": "strain=BUT-6", "accession": "GCA_024609805.1", "taxid": 1453545, "species_taxid": 1453545, "relation_to_type": "type", "validated": true, "ani": 78.3294, "matched_fragments": 354, "total_fragments": 1603, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004296575.1", "gtdb_species": "s__Dyella sp004296575", "ani": 100.0, "matched_fragments": 1602, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_016586165.1", "gtdb_species": "s__Dyella sp016586165", "ani": 87.5226, "matched_fragments": 1187, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_003264855.1", "gtdb_species": "s__Dyella jiangningensis_C", "ani": 87.4781, "matched_fragments": 1230, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_000632805.1", "gtdb_species": "s__Dyella jiangningensis", "ani": 86.8857, "matched_fragments": 1229, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_003332825.1", "gtdb_species": "s__Dyella sp003332825", "ani": 84.9088, "matched_fragments": 1004, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_003351225.1", "gtdb_species": "s__Dyella solisilvae", "ani": 84.7688, "matched_fragments": 1056, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_003201105.1", "gtdb_species": "s__Dyella jiangningensis_B", "ani": 84.6642, "matched_fragments": 1068, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_000725385.1", "gtdb_species": "s__Dyella japonica_C", "ani": 84.1532, "matched_fragments": 1052, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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_001010355.1", "gtdb_species": "s__Dyella japonica", "ani": 83.8178, "matched_fragments": 876, "total_fragments": 1603, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "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": -0.414, "cell_length": 0.291, "doubling_h": null, "growth_tmp": 28.444, "optimum_tmp": 29.444, "optimum_ph": 6.927, "genome_size": 4785947.716, "gc_content": 65.733, "coding_genes": 4123.333, "rRNA16S_genes": 2.0, "tRNA_genes": 50.666, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.888, "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": 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": [ "Dyella", "amyloliquefaciens" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }