{ "type": "genome", "identifier": "GCF_000685035.1", "organism": "Paraburkholderia ferrariae NBRC 106233", "title": "Paraburkholderia ferrariae NBRC 106233", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000685035.1", "bioproject": "PRJNA224116", "biosample": "SAMD00000356", "wgs_master": "BAYB00000000.1", "refseq_category": "reference genome", "taxid": "1218076", "species_taxid": "386056", "organism_name": "Paraburkholderia ferrariae NBRC 106233", "infraspecific_name": "strain=NBRC 106233", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/04/28", "asm_name": "ASM68503v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_000685035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/685/035/GCF_000685035.1_ASM68503v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7938642", "genome_size_ungapped": "7938642", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "97", "contig_count": "97", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000685035.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "7414", "protein_coding_gene_count": "7145", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-04-28", "dateModified": "2014-04-28", "datePublished": "2014-04-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Paraburkholderia ferrariae NBRC 106233" ], "sample_taxid": [ "1218076" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil:Minas Gerais" ], "sample_host_location_id": [], "data_size": "2.194 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)": "7938642", "Number of Sequences": "97", "Longest Sequences (bp)": "616475", "N50 (bp)": "223725", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.8", "Number of CDSs": "7213", "Average Protein Length": "310.9", "Coding Ratio (%)": "84.8", "Number of rRNAs": "2", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paraburkholderia ferrariae", "strain": "strain=NBRC 106233", "accession": "GCA_000685035.1", "taxid": 386056, "species_taxid": 386056, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2597, "total_fragments": 2602, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paraburkholderia acidipaludis", "strain": "strain=NBRC 101816", "accession": "GCA_000684975.1", "taxid": 660537, "species_taxid": 660537, "relation_to_type": "type", "validated": true, "ani": 87.3123, "matched_fragments": 1448, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia lycopersici", "strain": "strain=TNe-862", "accession": "GCA_900096975.1", "taxid": 416944, "species_taxid": 416944, "relation_to_type": "type", "validated": true, "ani": 85.1961, "matched_fragments": 1373, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia nodosa", "strain": "strain=DSM 21604", "accession": "GCA_000519185.1", "taxid": 392320, "species_taxid": 392320, "relation_to_type": "type", "validated": true, "ani": 85.0624, "matched_fragments": 1457, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia pallida", "strain": "strain=7MH5", "accession": "GCA_004524855.1", "taxid": 2547399, "species_taxid": 2547399, "relation_to_type": "type", "validated": true, "ani": 85.0424, "matched_fragments": 1463, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia oxyphila", "strain": "strain=NBRC 105797", "accession": "GCA_000685075.1", "taxid": 614212, "species_taxid": 614212, "relation_to_type": "type", "validated": true, "ani": 85.0353, "matched_fragments": 1444, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia heleia", "strain": "strain=NBRC 101817", "accession": "GCA_000739775.1", "taxid": 634127, "species_taxid": 634127, "relation_to_type": "type", "validated": true, "ani": 85.0224, "matched_fragments": 1412, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia guartelaensis", "strain": "strain=CNPSo 3008", "accession": "GCA_004353905.1", "taxid": 2546446, "species_taxid": 2546446, "relation_to_type": "type", "validated": true, "ani": 84.9578, "matched_fragments": 1462, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia acidiphila", "strain": "strain=7Q-K02", "accession": "GCA_009789655.1", "taxid": 2571747, "species_taxid": 2571747, "relation_to_type": "type", "validated": true, "ani": 84.9029, "matched_fragments": 1403, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia silviterrae", "strain": "strain=4M-K11", "accession": "GCA_004353915.1", "taxid": 2528715, "species_taxid": 2528715, "relation_to_type": "type", "validated": true, "ani": 84.8593, "matched_fragments": 1401, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia sacchari", "strain": "strain=LMG 19450", "accession": "GCA_902833715.1", "taxid": 159450, "species_taxid": 159450, "relation_to_type": "type", "validated": true, "ani": 84.8367, "matched_fragments": 1281, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia dinghuensis", "strain": "strain=DHOA04", "accession": "GCA_003837865.1", "taxid": 2305225, "species_taxid": 2305225, "relation_to_type": "type", "validated": true, "ani": 84.7845, "matched_fragments": 1149, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia mimosarum", "strain": "strain=NBRC 106338", "accession": "GCA_000739815.1", "taxid": 312026, "species_taxid": 312026, "relation_to_type": "type", "validated": true, "ani": 84.7004, "matched_fragments": 1321, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia acidisoli", "strain": "strain=DHF22", "accession": "GCA_009789675.1", "taxid": 2571748, "species_taxid": 2571748, "relation_to_type": "type", "validated": true, "ani": 84.6701, "matched_fragments": 1395, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia hiiakae", "strain": "strain=LMG 27952", "accession": "GCA_904848665.1", "taxid": 1081782, "species_taxid": 1081782, "relation_to_type": "type", "validated": true, "ani": 84.5624, "matched_fragments": 1412, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia bannensis", "strain": "strain=NBRC 103871", "accession": "GCA_000685015.1", "taxid": 765414, "species_taxid": 765414, "relation_to_type": "type", "validated": true, "ani": 84.2417, "matched_fragments": 1414, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia podalyriae", "strain": "strain=WC7.3b", "accession": "GCA_014397785.1", "taxid": 1938811, "species_taxid": 1938811, "relation_to_type": "type", "validated": true, "ani": 81.4928, "matched_fragments": 1110, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia perseverans", "strain": "strain=INN12", "accession": "GCA_022870505.1", "taxid": 2615214, "species_taxid": 2615214, "relation_to_type": "type", "validated": true, "ani": 81.4882, "matched_fragments": 1067, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia azotifigens", "strain": "strain=NF 2-5-3", "accession": "GCA_007995085.1", "taxid": 2057004, "species_taxid": 2057004, "relation_to_type": "type", "validated": true, "ani": 81.2889, "matched_fragments": 1140, "total_fragments": 2602, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000685035.1", "gtdb_species": "s__Paraburkholderia ferrariae", "ani": 100.0, "matched_fragments": 2597, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_000684975.1", "gtdb_species": "s__Paraburkholderia acidipaludis", "ani": 87.3372, "matched_fragments": 1444, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_900096975.1", "gtdb_species": "s__Paraburkholderia lycopersici", "ani": 85.1434, "matched_fragments": 1380, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_000519185.1", "gtdb_species": "s__Paraburkholderia nodosa", "ani": 85.0837, "matched_fragments": 1454, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_000739775.1", "gtdb_species": "s__Paraburkholderia heleia", "ani": 85.034, "matched_fragments": 1410, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.5542, "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_003096715.1", "gtdb_species": "s__Paraburkholderia silvatlantica", "ani": 85.0273, "matched_fragments": 1409, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.5542, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.23", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003268775.1", "gtdb_species": "s__Paraburkholderia unamae", "ani": 85.0078, "matched_fragments": 1512, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "98.69", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000685075.1", "gtdb_species": "s__Paraburkholderia oxyphila", "ani": 85.0034, "matched_fragments": 1450, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.32", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.74", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001718195.1", "gtdb_species": "s__Paraburkholderia nodosa_A", "ani": 84.9908, "matched_fragments": 1424, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_009789655.1", "gtdb_species": "s__Paraburkholderia acidiphila", "ani": 84.9157, "matched_fragments": 1401, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_004353915.1", "gtdb_species": "s__Paraburkholderia sp004353915", "ani": 84.8931, "matched_fragments": 1397, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_000785435.2", "gtdb_species": "s__Paraburkholderia sacchari", "ani": 84.8005, "matched_fragments": 1292, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "96.11", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003837865.1", "gtdb_species": "s__Paraburkholderia dinghuensis", "ani": 84.7737, "matched_fragments": 1150, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_009789675.1", "gtdb_species": "s__Paraburkholderia acidisoli", "ani": 84.6262, "matched_fragments": 1402, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_904848665.1", "gtdb_species": "s__Paraburkholderia hiiakae", "ani": 84.5702, "matched_fragments": 1411, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_000685015.1", "gtdb_species": "s__Paraburkholderia bannensis", "ani": 84.2411, "matched_fragments": 1414, "total_fragments": 2602, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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": -0.206, "cell_length": 0.138, "doubling_h": 0.0, "growth_tmp": 28.5, "optimum_tmp": 29.643, "optimum_ph": 6.11, "genome_size": 7938642.0, "gc_content": 64.8, "coding_genes": 7196.441, "rRNA16S_genes": 5.571, "tRNA_genes": 61.73, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.689, "range_salinity": 0.5, "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": [ "Paraburkholderia", "ferrariae", "NBRC", "106233" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }