{ "type": "genome", "identifier": "GCF_020099355.1", "organism": "Burkholderia vietnamiensis", "title": "Burkholderia vietnamiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020099355.1", "bioproject": "PRJNA224116", "biosample": "SAMN21218844", "wgs_master": "na", "refseq_category": "na", "taxid": "60552", "species_taxid": "60552", "organism_name": "Burkholderia vietnamiensis", "infraspecific_name": "strain=FDAARGOS_1488", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/09/23", "asm_name": "ASM2009935v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_020099355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/099/355/GCF_020099355.1_ASM2009935v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6930499", "genome_size_ungapped": "6930499", "gc_percent": "67.000000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020099355.1-RS_2024_03_30", "annotation_date": "2024-03-30", "total_gene_count": "6286", "protein_coding_gene_count": "6053", "non_coding_gene_count": "93", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-09-23", "dateModified": "2021-09-23", "datePublished": "2021-09-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Burkholderia vietnamiensis" ], "sample_taxid": [ "60552" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Braunschweig" ], "sample_host_location_id": [], "data_size": "1.867 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)": "6930499", "Number of Sequences": "4", "Longest Sequences (bp)": "3317416", "N50 (bp)": "2262096", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.8", "Number of CDSs": "6180", "Average Protein Length": "318.9", "Coding Ratio (%)": "85.3", "Number of rRNAs": "18", "Number of tRNAs": "76", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Burkholderia vietnamiensis", "strain": "strain=FDAARGOS_1488", "accession": "GCA_020099355.1", "taxid": 60552, "species_taxid": 60552, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2309, "total_fragments": 2309, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Burkholderia vietnamiensis", "strain": "strain=LMG 10929", "accession": "GCA_000959445.1", "taxid": 60552, "species_taxid": 60552, "relation_to_type": "type", "validated": true, "ani": 99.9959, "matched_fragments": 2308, "total_fragments": 2309, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Burkholderia vietnamiensis", "strain": "strain=LMG 10929", "accession": "GCA_902830295.1", "taxid": 60552, "species_taxid": 60552, "relation_to_type": "type", "validated": true, "ani": 99.9802, "matched_fragments": 2265, "total_fragments": 2309, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Burkholderia latens", "strain": "", "accession": "GCA_902499045.1", "taxid": 488446, "species_taxid": 488446, "relation_to_type": "suspected-type", "validated": true, "ani": 90.5959, "matched_fragments": 1621, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia latens", "strain": "strain=CCUG 54555", "accession": "GCA_008802135.1", "taxid": 488446, "species_taxid": 488446, "relation_to_type": "suspected-type", "validated": true, "ani": 90.4936, "matched_fragments": 1571, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia territorii", "strain": "strain=LMG 28158", "accession": "GCA_902833055.1", "taxid": 1503055, "species_taxid": 1503055, "relation_to_type": "type", "validated": true, "ani": 90.3994, "matched_fragments": 1648, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia territorii", "strain": "", "accession": "GCA_902499035.1", "taxid": 1503055, "species_taxid": 1503055, "relation_to_type": "type", "validated": true, "ani": 90.3768, "matched_fragments": 1629, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia anthina", "strain": "strain=DSM 16086", "accession": "GCA_016836725.1", "taxid": 179879, "species_taxid": 179879, "relation_to_type": "suspected-type", "validated": true, "ani": 90.0398, "matched_fragments": 1613, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia territorii", "strain": "strain=CCUG 65687", "accession": "GCA_008802115.1", "taxid": 1503055, "species_taxid": 1503055, "relation_to_type": "type", "validated": true, "ani": 89.9753, "matched_fragments": 1150, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia ubonensis", "strain": "strain=LMG 20358", "accession": "GCA_902833085.1", "taxid": 101571, "species_taxid": 101571, "relation_to_type": "type", "validated": true, "ani": 88.0642, "matched_fragments": 1583, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Burkholderia ubonensis", "strain": "", "accession": "GCA_902499185.1", "taxid": 101571, "species_taxid": 101571, "relation_to_type": "type", "validated": true, "ani": 88.0051, "matched_fragments": 1543, "total_fragments": 2309, "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": 83.7329, "matched_fragments": 1338, "total_fragments": 2309, "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": 81.7799, "matched_fragments": 1134, "total_fragments": 2309, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000959445.1", "gtdb_species": "s__Burkholderia vietnamiensis", "ani": 99.9959, "matched_fragments": 2308, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 111, "status": "conclusive" }, { "accession": "GCF_000949135.2", "gtdb_species": "s__Burkholderia sp000949135", "ani": 90.7364, "matched_fragments": 1685, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.85", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_003853415.1", "gtdb_species": "s__Burkholderia sp003853415", "ani": 90.6976, "matched_fragments": 1675, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "99.32", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_902499045.1", "gtdb_species": "s__Burkholderia latens", "ani": 90.5677, "matched_fragments": 1624, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003853645.1", "gtdb_species": "s__Burkholderia sp003853645", "ani": 90.5589, "matched_fragments": 1642, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.08", "min_intra_species_ani": "96.08", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.79", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000292915.1", "gtdb_species": "s__Burkholderia cepacia_D", "ani": 90.527, "matched_fragments": 1520, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "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_003635165.1", "gtdb_species": "s__Burkholderia sp003635165", "ani": 90.4351, "matched_fragments": 1684, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "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_902833055.1", "gtdb_species": "s__Burkholderia territorii", "ani": 90.4188, "matched_fragments": 1645, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.1139, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 37, "status": "-" }, { "accession": "GCF_000203915.1", "gtdb_species": "s__Burkholderia ambifaria", "ani": 90.417, "matched_fragments": 1714, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.41", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.79", "num_clustered_genomes": 83, "status": "-" }, { "accession": "GCF_902499115.1", "gtdb_species": "s__Burkholderia diffusa", "ani": 90.3585, "matched_fragments": 1667, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001443045.1", "gtdb_species": "s__Burkholderia ambifaria_A", "ani": 90.3213, "matched_fragments": 1671, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001718315.1", "gtdb_species": "s__Burkholderia diffusa_B", "ani": 90.1033, "matched_fragments": 1704, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.1139, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_902498995.1", "gtdb_species": "s__Burkholderia anthina", "ani": 90.0159, "matched_fragments": 1617, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.57", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.77", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_902833145.1", "gtdb_species": "s__Burkholderia sp902833145", "ani": 89.743, "matched_fragments": 1659, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016899425.1", "gtdb_species": "s__Burkholderia sp002223185", "ani": 89.656, "matched_fragments": 1730, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.84", "num_clustered_genomes": 68, "status": "-" }, { "accession": "GCF_001522585.2", "gtdb_species": "s__Burkholderia sp001522585", "ani": 89.6526, "matched_fragments": 1668, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.44", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.83", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001718835.1", "gtdb_species": "s__Burkholderia cepacia_F", "ani": 88.9153, "matched_fragments": 1611, "total_fragments": 2309, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia", "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": -0.523, "cell_length": -0.097, "doubling_h": -0.157, "growth_tmp": 29.0, "optimum_tmp": 37.0, "optimum_ph": 7.1, "genome_size": 6944837.113, "gc_content": 64.364, "coding_genes": 6312.556, "rRNA16S_genes": 6.0, "tRNA_genes": 67.571, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.25, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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": [ "Burkholderia", "vietnamiensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }