{ "type": "genome", "identifier": "GCF_900112675.1", "organism": "Paracidovorax konjaci", "title": "Paracidovorax konjaci", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900112675.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489710", "wgs_master": "FOMQ00000000.1", "refseq_category": "reference genome", "taxid": "32040", "species_taxid": "32040", "organism_name": "Paracidovorax konjaci", "infraspecific_name": "strain=DSM 7481", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2634166315 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900112675.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/112/675/GCF_900112675.1_IMG-taxon_2634166315_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": "5077528", "genome_size_ungapped": "5076563", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "36", "contig_count": "36", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900112675.1-RS_2024_07_01", "annotation_date": "2024-07-01", "total_gene_count": "4591", "protein_coding_gene_count": "4491", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Paracidovorax konjaci" ], "sample_taxid": [ "32040" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.386 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5077528", "Number of Sequences": "36", "Longest Sequences (bp)": "612984", "N50 (bp)": "369808", "Gap Ratio (%)": "0.019005", "GCcontent (%)": "68.2", "Number of CDSs": "4476", "Average Protein Length": "336.8", "Coding Ratio (%)": "89.1", "Number of rRNAs": "5", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Acidovorax konjaci", "strain": "strain=DSM 7481", "accession": "GCA_900112675.1", "taxid": 32040, "species_taxid": 32040, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1673, "total_fragments": 1674, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Acidovorax anthurii", "strain": "strain=CFPB 3232", "accession": "GCA_003269065.1", "taxid": 78229, "species_taxid": 78229, "relation_to_type": "type", "validated": true, "ani": 87.3814, "matched_fragments": 1250, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax citrulli", "strain": "strain=DSM 17060", "accession": "GCA_900100305.1", "taxid": 80869, "species_taxid": 80869, "relation_to_type": "type", "validated": true, "ani": 86.0008, "matched_fragments": 1186, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax avenae subsp. avenae", "strain": "strain=ATCC 19860", "accession": "GCA_000176855.2", "taxid": 80870, "species_taxid": 80867, "relation_to_type": "suspected-type", "validated": true, "ani": 85.7973, "matched_fragments": 1269, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax oryzae", "strain": "strain=ATCC 19882", "accession": "GCA_000687165.1", "taxid": 862720, "species_taxid": 862720, "relation_to_type": "type", "validated": true, "ani": 85.6884, "matched_fragments": 1270, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax cattleyae", "strain": "strain=DSM 17101", "accession": "GCA_900104515.1", "taxid": 80868, "species_taxid": 80868, "relation_to_type": "type", "validated": true, "ani": 85.6729, "matched_fragments": 1280, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax valerianellae", "strain": "strain=DSM 16619", "accession": "GCA_900102625.1", "taxid": 187868, "species_taxid": 187868, "relation_to_type": "type", "validated": true, "ani": 83.1124, "matched_fragments": 1092, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax facilis", "strain": "strain=DSM 649", "accession": "GCA_023913775.1", "taxid": 12917, "species_taxid": 12917, "relation_to_type": "type", "validated": true, "ani": 80.8008, "matched_fragments": 820, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga crocea", "strain": "strain=BA0156", "accession": "GCA_011388215.1", "taxid": 2716225, "species_taxid": 2716225, "relation_to_type": "type", "validated": true, "ani": 80.2692, "matched_fragments": 658, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xylophilus ampelinus", "strain": "strain=CFBP 1192", "accession": "GCA_024832295.1", "taxid": 54067, "species_taxid": 54067, "relation_to_type": "type", "validated": true, "ani": 80.1066, "matched_fragments": 640, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Diaphorobacter caeni", "strain": "strain=NR2-3-3-1", "accession": "GCA_015354245.1", "taxid": 2784387, "species_taxid": 2784387, "relation_to_type": "type", "validated": true, "ani": 80.0112, "matched_fragments": 724, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter humi", "strain": "strain=18x22-1", "accession": "GCA_004681975.1", "taxid": 2530451, "species_taxid": 2530451, "relation_to_type": "type", "validated": true, "ani": 79.9534, "matched_fragments": 644, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corticibacter populi", "strain": "strain=DSM 105136", "accession": "GCA_004217315.1", "taxid": 1550736, "species_taxid": 1550736, "relation_to_type": "type", "validated": true, "ani": 78.7786, "matched_fragments": 451, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corticibacter populi", "strain": "strain=DSM 105136", "accession": "GCA_003703815.1", "taxid": 1550736, "species_taxid": 1550736, "relation_to_type": "type", "validated": true, "ani": 78.6868, "matched_fragments": 459, "total_fragments": 1674, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900112675.1", "gtdb_species": "s__Acidovorax_A konjaci", "ani": 100.0, "matched_fragments": 1673, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "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_003269065.1", "gtdb_species": "s__Acidovorax_A anthurii", "ani": 87.3743, "matched_fragments": 1251, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "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_002397315.1", "gtdb_species": "s__Acidovorax_A sp002397315", "ani": 86.3482, "matched_fragments": 1204, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "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_900100305.1", "gtdb_species": "s__Acidovorax_A citrulli", "ani": 86.0014, "matched_fragments": 1186, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_000176855.2", "gtdb_species": "s__Acidovorax_A avenae", "ani": 85.8222, "matched_fragments": 1266, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "ani_circumscription_radius": 95.2137, "mean_intra_species_ani": "96.92", "min_intra_species_ani": "95.92", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.51", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_000687165.1", "gtdb_species": "s__Acidovorax_A oryzae", "ani": 85.7077, "matched_fragments": 1268, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "ani_circumscription_radius": 95.2137, "mean_intra_species_ani": "98.08", "min_intra_species_ani": "98.08", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900104515.1", "gtdb_species": "s__Acidovorax_A cattleyae", "ani": 85.6928, "matched_fragments": 1277, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001424265.1", "gtdb_species": "s__Acidovorax_A sp001424265", "ani": 83.2256, "matched_fragments": 980, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "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_900102625.1", "gtdb_species": "s__Acidovorax_A valerianellae", "ani": 83.1027, "matched_fragments": 1094, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A", "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_004217315.1", "gtdb_species": "s__Lampropedia populi", "ani": 78.7882, "matched_fragments": 450, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia", "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": "GCA_019234815.1", "gtdb_species": "s__WAJ17 sp019234815", "ani": 78.7004, "matched_fragments": 364, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17", "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_002837135.1", "gtdb_species": "s__Macromonas bipunctata", "ani": 78.5261, "matched_fragments": 321, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Macromonas", "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_016718405.1", "gtdb_species": "s__Rhodoferax sp016718405", "ani": 77.7411, "matched_fragments": 340, "total_fragments": 1674, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.26", "min_intra_species_ani": "98.26", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "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": [ "Paracidovorax", "konjaci" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }