{ "type": "genome", "identifier": "GCF_902833515.1", "organism": "Paraburkholderia caribensis", "title": "Paraburkholderia caribensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CARDIFF SCHOOL OF BIOSCIENCES", "publication": [ {} ], "properties": { "assembly_accession": "GCF_902833515.1", "bioproject": "PRJNA224116", "biosample": "SAMEA6503609", "wgs_master": "CADFFM000000000.1", "refseq_category": "na", "taxid": "75105", "species_taxid": "75105", "organism_name": "Paraburkholderia caribensis", "infraspecific_name": "strain=LMG 18531", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/09", "asm_name": "ASM90283351v1", "asm_submitter": "CARDIFF SCHOOL OF BIOSCIENCES", "gbrs_paired_asm": "GCA_902833515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/833/515/GCF_902833515.1_ASM90283351v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8968349", "genome_size_ungapped": "8966982", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "76", "contig_count": "76", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-18", "total_gene_count": "8065", "protein_coding_gene_count": "7833", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-09", "dateModified": "2020-06-09", "datePublished": "2020-06-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Paraburkholderia caribensis" ], "sample_taxid": [ "75105" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "2.483 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)": "8968349", "Number of Sequences": "76", "Longest Sequences (bp)": "808120", "N50 (bp)": "301636", "Gap Ratio (%)": "0.015309", "GCcontent (%)": "62.6", "Number of CDSs": "7939", "Average Protein Length": "316.9", "Coding Ratio (%)": "84.2", "Number of rRNAs": "3", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paraburkholderia caribensis", "strain": "strain=LMG 18531", "accession": "GCA_902833515.1", "taxid": 75105, "species_taxid": 75105, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2962, "total_fragments": 2963, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paraburkholderia caribensis", "strain": "strain=DSM 13236", "accession": "GCA_002902945.1", "taxid": 75105, "species_taxid": 75105, "relation_to_type": "type", "validated": true, "ani": 99.9947, "matched_fragments": 2960, "total_fragments": 2963, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paraburkholderia caribensis", "strain": "strain=MWAP64", "accession": "GCA_001449005.1", "taxid": 75105, "species_taxid": 75105, "relation_to_type": "type", "validated": true, "ani": 99.9923, "matched_fragments": 2961, "total_fragments": 2963, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paraburkholderia terrae", "strain": "strain=NBRC 100964", "accession": "GCA_000739835.1", "taxid": 311230, "species_taxid": 311230, "relation_to_type": "type", "validated": true, "ani": 92.9344, "matched_fragments": 2233, "total_fragments": 2963, "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": 92.8693, "matched_fragments": 2341, "total_fragments": 2963, "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": 92.8603, "matched_fragments": 2332, "total_fragments": 2963, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia hospita", "strain": "strain=DSM 17164", "accession": "GCA_002902965.1", "taxid": 169430, "species_taxid": 169430, "relation_to_type": "type", "validated": true, "ani": 92.7703, "matched_fragments": 2357, "total_fragments": 2963, "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": 87.8244, "matched_fragments": 2193, "total_fragments": 2963, "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": 82.5167, "matched_fragments": 1176, "total_fragments": 2963, "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": 82.3851, "matched_fragments": 1299, "total_fragments": 2963, "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": 82.1412, "matched_fragments": 1237, "total_fragments": 2963, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia kirstenboschensis", "strain": "strain=KB15", "accession": "GCA_001636975.1", "taxid": 1245436, "species_taxid": 1245436, "relation_to_type": "type", "validated": true, "ani": 81.5292, "matched_fragments": 1108, "total_fragments": 2963, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002902945.1", "gtdb_species": "s__Paraburkholderia caribensis", "ani": 99.9947, "matched_fragments": 2960, "total_fragments": 2963, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "96.01", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.80", "num_clustered_genomes": 9, "status": "conclusive" }, { "accession": "GCF_002902925.1", "gtdb_species": "s__Paraburkholderia terrae", "ani": 92.8697, "matched_fragments": 2340, "total_fragments": 2963, "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_002902965.1", "gtdb_species": "s__Paraburkholderia hospita", "ani": 92.7473, "matched_fragments": 2360, "total_fragments": 2963, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.2599, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "97.70", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_013426915.1", "gtdb_species": "s__Paraburkholderia sp013426915", "ani": 92.4573, "matched_fragments": 2276, "total_fragments": 2963, "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_013426895.1", "gtdb_species": "s__Paraburkholderia sp013426895", "ani": 92.0157, "matched_fragments": 2352, "total_fragments": 2963, "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": 88.5095, "matched_fragments": 2190, "total_fragments": 2963, "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": -0.302, "cell_length": 0.0, "doubling_h": 0.0, "growth_tmp": 28.5, "optimum_tmp": 28.8, "optimum_ph": 6.11, "genome_size": 9263541.9, "gc_content": 62.08, "coding_genes": 8151.0, "rRNA16S_genes": 6.0, "tRNA_genes": 62.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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", "caribensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }