{ "type": "genome", "identifier": "GCF_904848645.1", "organism": "Paraburkholderia sabiae", "title": "Paraburkholderia sabiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "LM-UGent", "publication": [ {} ], "properties": { "assembly_accession": "GCF_904848645.1", "bioproject": "PRJNA224116", "biosample": "SAMEA7384720", "wgs_master": "CAJHCS000000000.1", "refseq_category": "na", "taxid": "273251", "species_taxid": "273251", "organism_name": "Paraburkholderia sabiae", "infraspecific_name": "strain=LMG 24235", "isolate": "LMG 24235", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/11/22", "asm_name": "LMG 24235", "asm_submitter": "LM-UGent", "gbrs_paired_asm": "GCA_904848645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/904/848/645/GCF_904848645.1_LMG_24235", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9749118", "genome_size_ungapped": "9749118", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "161", "contig_count": "161", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_904848645.1-RS_2024_12_23", "annotation_date": "2024-12-23", "total_gene_count": "8853", "protein_coding_gene_count": "8546", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-11-22", "dateModified": "2020-11-22", "datePublished": "2020-11-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Paraburkholderia sabiae" ], "sample_taxid": [ "273251" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "2.699 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)": "9749118", "Number of Sequences": "161", "Longest Sequences (bp)": "1040461", "N50 (bp)": "207876", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.1", "Number of CDSs": "8683", "Average Protein Length": "316.9", "Coding Ratio (%)": "84.7", "Number of rRNAs": "2", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paraburkholderia sabiae", "strain": "strain=LMG 24235", "accession": "GCA_904848645.1", "taxid": 273251, "species_taxid": 273251, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 3165, "total_fragments": 3170, "ani_threshold": 95, "status": "conclusive" }, { "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": 91.7636, "matched_fragments": 2401, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia phymatum", "strain": "strain=LMG 21445", "accession": "GCA_902833665.1", "taxid": 148447, "species_taxid": 148447, "relation_to_type": "type", "validated": true, "ani": 89.1523, "matched_fragments": 2105, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia phymatum", "strain": "strain=STM815", "accession": "GCA_000020045.1", "taxid": 148447, "species_taxid": 148447, "relation_to_type": "type", "validated": true, "ani": 89.1075, "matched_fragments": 2117, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia terrae", "strain": "strain=NBRC 100964", "accession": "GCA_000739835.1", "taxid": 311230, "species_taxid": 311230, "relation_to_type": "type", "validated": true, "ani": 88.2734, "matched_fragments": 2135, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia terrae", "strain": "strain=DSM 17804", "accession": "GCA_002902925.1", "taxid": 311230, "species_taxid": 311230, "relation_to_type": "type", "validated": true, "ani": 88.2076, "matched_fragments": 2211, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia hospita", "strain": "strain=LMG 20598", "accession": "GCA_902833685.1", "taxid": 169430, "species_taxid": 169430, "relation_to_type": "type", "validated": true, "ani": 88.1094, "matched_fragments": 2226, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia caribensis", "strain": "strain=LMG 18531", "accession": "GCA_902833515.1", "taxid": 75105, "species_taxid": 75105, "relation_to_type": "type", "validated": true, "ani": 88.0285, "matched_fragments": 2088, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia caribensis", "strain": "strain=DSM 13236", "accession": "GCA_002902945.1", "taxid": 75105, "species_taxid": 75105, "relation_to_type": "type", "validated": true, "ani": 88.0184, "matched_fragments": 2122, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia piptadeniae", "strain": "strain=STM 7183", "accession": "GCA_900007165.2", "taxid": 1701573, "species_taxid": 1701573, "relation_to_type": "type", "validated": true, "ani": 87.0916, "matched_fragments": 1870, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia flava", "strain": "strain=LD6", "accession": "GCA_004359985.1", "taxid": 2547393, "species_taxid": 2547393, "relation_to_type": "type", "validated": true, "ani": 82.9334, "matched_fragments": 1333, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia gardini", "strain": "strain=LMG 32171", "accession": "GCA_907164575.1", "taxid": 2823469, "species_taxid": 2823469, "relation_to_type": "type", "validated": true, "ani": 82.6012, "matched_fragments": 1238, "total_fragments": 3170, "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": 82.5305, "matched_fragments": 1424, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia domus", "strain": "strain=LMG 31832", "accession": "GCA_905220705.1", "taxid": 2793075, "species_taxid": 2793075, "relation_to_type": "type", "validated": true, "ani": 81.7042, "matched_fragments": 1344, "total_fragments": 3170, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_904848645.1", "gtdb_species": "s__Paraburkholderia sabiae", "ani": 100.0, "matched_fragments": 3165, "total_fragments": 3170, "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_007995085.1", "gtdb_species": "s__Paraburkholderia azotifigens", "ani": 91.7723, "matched_fragments": 2400, "total_fragments": 3170, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017104565.1", "gtdb_species": "s__Paraburkholderia sp017104565", "ani": 90.67, "matched_fragments": 2260, "total_fragments": 3170, "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_000020045.1", "gtdb_species": "s__Paraburkholderia phymatum", "ani": 89.1214, "matched_fragments": 2115, "total_fragments": 3170, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "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_002902925.1", "gtdb_species": "s__Paraburkholderia terrae", "ani": 88.1901, "matched_fragments": 2213, "total_fragments": 3170, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.2599, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013426895.1", "gtdb_species": "s__Paraburkholderia sp013426895", "ani": 88.1326, "matched_fragments": 2213, "total_fragments": 3170, "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_017104715.1", "gtdb_species": "s__Paraburkholderia sp017104715", "ani": 87.9413, "matched_fragments": 2157, "total_fragments": 3170, "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_003121405.1", "gtdb_species": "s__Paraburkholderia sp003121405", "ani": 87.3793, "matched_fragments": 1947, "total_fragments": 3170, "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_900007165.1", "gtdb_species": "s__Paraburkholderia piptadeniae", "ani": 87.0916, "matched_fragments": 1869, "total_fragments": 3170, "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": "GCA_001319865.1", "gtdb_species": "s__Paraburkholderia sp001319865", "ani": 86.7917, "matched_fragments": 1705, "total_fragments": 3170, "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": -0.398, "cell_length": -0.222, "doubling_h": 0.0, "growth_tmp": 30.0, "optimum_tmp": 28.0, "optimum_ph": 7.0, "genome_size": 7672919.331, "gc_content": 62.985, "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", "sabiae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }