{ "type": "genome", "identifier": "GCF_002917095.1", "organism": "Paraburkholderia eburnea", "title": "Paraburkholderia eburnea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002917095.1", "bioproject": "PRJNA224116", "biosample": "SAMN06295901", "wgs_master": "PQGA00000000.1", "refseq_category": "na", "taxid": "1189126", "species_taxid": "1189126", "organism_name": "Paraburkholderia eburnea", "infraspecific_name": "strain=JCM 18070", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/02/05", "asm_name": "ASM291709v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_002917095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/917/095/GCF_002917095.1_ASM291709v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6947977", "genome_size_ungapped": "6947286", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002917095.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "6274", "protein_coding_gene_count": "6101", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-02-05", "dateModified": "2018-02-05", "datePublished": "2018-02-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Paraburkholderia eburnea" ], "sample_taxid": [ "1189126" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.919 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)": "6947977", "Number of Sequences": "58", "Longest Sequences (bp)": "983781", "N50 (bp)": "294829", "Gap Ratio (%)": "0.009945", "GCcontent (%)": "64.1", "Number of CDSs": "6154", "Average Protein Length": "324.3", "Coding Ratio (%)": "86.2", "Number of rRNAs": "2", "Number of tRNAs": "61", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paraburkholderia eburnea", "strain": "strain=JCM 18070", "accession": "GCA_002917095.1", "taxid": 1189126, "species_taxid": 1189126, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2284, "total_fragments": 2286, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paraburkholderia bannensis", "strain": "strain=NBRC 103871", "accession": "GCA_000685015.1", "taxid": 765414, "species_taxid": 765414, "relation_to_type": "type", "validated": true, "ani": 90.2165, "matched_fragments": 1814, "total_fragments": 2286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia tropica", "strain": "strain=LMG 22274", "accession": "GCA_900109265.1", "taxid": 92647, "species_taxid": 92647, "relation_to_type": "type", "validated": true, "ani": 86.79, "matched_fragments": 1625, "total_fragments": 2286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia tropica", "strain": "strain=Ppe8", "accession": "GCA_002071575.1", "taxid": 92647, "species_taxid": 92647, "relation_to_type": "type", "validated": true, "ani": 86.7829, "matched_fragments": 1642, "total_fragments": 2286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia tropica", "strain": "strain=LMG 22274", "accession": "GCA_902833865.1", "taxid": 92647, "species_taxid": 92647, "relation_to_type": "type", "validated": true, "ani": 86.7625, "matched_fragments": 1639, "total_fragments": 2286, "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": 86.06, "matched_fragments": 1578, "total_fragments": 2286, "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": 86.0593, "matched_fragments": 1528, "total_fragments": 2286, "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": 85.9746, "matched_fragments": 1560, "total_fragments": 2286, "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": 85.745, "matched_fragments": 1379, "total_fragments": 2286, "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": 85.2617, "matched_fragments": 1444, "total_fragments": 2286, "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": 84.7804, "matched_fragments": 1469, "total_fragments": 2286, "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": 81.4614, "matched_fragments": 1082, "total_fragments": 2286, "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": 81.3033, "matched_fragments": 1169, "total_fragments": 2286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia saeva", "strain": "strain=LMG 31841", "accession": "GCA_907164555.1", "taxid": 2777537, "species_taxid": 2777537, "relation_to_type": "type", "validated": true, "ani": 81.0978, "matched_fragments": 975, "total_fragments": 2286, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002917095.1", "gtdb_species": "s__Paraburkholderia eburnea", "ani": 100.0, "matched_fragments": 2284, "total_fragments": 2286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000685015.1", "gtdb_species": "s__Paraburkholderia bannensis", "ani": 90.2044, "matched_fragments": 1816, "total_fragments": 2286, "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_011753055.1", "gtdb_species": "s__Paraburkholderia sp011753055", "ani": 89.7288, "matched_fragments": 1806, "total_fragments": 2286, "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_014200455.1", "gtdb_species": "s__Paraburkholderia bannensis_A", "ani": 89.4912, "matched_fragments": 1765, "total_fragments": 2286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_017104965.1", "gtdb_species": "s__Paraburkholderia sp017104965", "ani": 88.8192, "matched_fragments": 1760, "total_fragments": 2286, "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_900109265.1", "gtdb_species": "s__Paraburkholderia tropica", "ani": 86.8204, "matched_fragments": 1621, "total_fragments": 2286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.07", "min_intra_species_ani": "95.97", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_009789675.1", "gtdb_species": "s__Paraburkholderia acidisoli", "ani": 85.2728, "matched_fragments": 1442, "total_fragments": 2286, "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_003268775.1", "gtdb_species": "s__Paraburkholderia unamae", "ani": 85.2323, "matched_fragments": 1489, "total_fragments": 2286, "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_904848665.1", "gtdb_species": "s__Paraburkholderia hiiakae", "ani": 84.7742, "matched_fragments": 1471, "total_fragments": 2286, "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": 30.0, "optimum_tmp": 29.643, "optimum_ph": 6.11, "genome_size": 6949552.0, "gc_content": 62.985, "coding_genes": 7196.441, "rRNA16S_genes": 5.571, "tRNA_genes": 61.73, "gram_stain": 0.0, "sporulation": 0.035, "motility": 0.689, "range_salinity": 0.5, "facultative_respiration": 0.029, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.97, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.945, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.054, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Paraburkholderia", "eburnea" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }