{ "type": "genome", "identifier": "GCF_902833645.1", "organism": "Paraburkholderia fungorum", "title": "Paraburkholderia fungorum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CARDIFF SCHOOL OF BIOSCIENCES", "publication": [ {} ], "properties": { "assembly_accession": "GCF_902833645.1", "bioproject": "PRJNA224116", "biosample": "SAMEA6503610", "wgs_master": "CADFGE000000000.1", "refseq_category": "na", "taxid": "134537", "species_taxid": "134537", "organism_name": "Paraburkholderia fungorum", "infraspecific_name": "strain=LMG 16225", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/09", "asm_name": "ASM90283364v1", "asm_submitter": "CARDIFF SCHOOL OF BIOSCIENCES", "gbrs_paired_asm": "GCA_902833645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/833/645/GCF_902833645.1_ASM90283364v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8926561", "genome_size_ungapped": "8926198", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_902833645.1-RS_2024_04_20", "annotation_date": "2024-04-20", "total_gene_count": "8146", "protein_coding_gene_count": "7965", "non_coding_gene_count": "64", "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 fungorum" ], "sample_taxid": [ "134537" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "2.493 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8926561", "Number of Sequences": "33", "Longest Sequences (bp)": "1509393", "N50 (bp)": "451759", "Gap Ratio (%)": "0.004078", "GCcontent (%)": "61.8", "Number of CDSs": "8104", "Average Protein Length": "313.6", "Coding Ratio (%)": "85.4", "Number of rRNAs": "2", "Number of tRNAs": "66", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paraburkholderia fungorum", "strain": "strain=LMG 16225", "accession": "GCA_902833645.1", "taxid": 134537, "species_taxid": 134537, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 2961, "total_fragments": 2962, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Paraburkholderia fungorum", "strain": "strain=NBRC 102489", "accession": "GCA_000685055.1", "taxid": 134537, "species_taxid": 134537, "relation_to_type": "type", "validated": true, "ani": 99.9768, "matched_fragments": 2829, "total_fragments": 2962, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Paraburkholderia fungorum", "strain": "strain=ATCC BAA-463", "accession": "GCA_000961515.1", "taxid": 134537, "species_taxid": 134537, "relation_to_type": "suspected-type", "validated": true, "ani": 98.5399, "matched_fragments": 2597, "total_fragments": 2962, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Paraburkholderia agricolaris", "strain": "strain=BaQS159", "accession": "GCA_009455635.1", "taxid": 2152888, "species_taxid": 2152888, "relation_to_type": "type", "validated": true, "ani": 95.5818, "matched_fragments": 2174, "total_fragments": 2962, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Paraburkholderia elongata", "strain": "strain=5N", "accession": "GCA_013177735.1", "taxid": 2675747, "species_taxid": 2675747, "relation_to_type": "type", "validated": true, "ani": 89.7832, "matched_fragments": 1795, "total_fragments": 2962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia haematera", "strain": "strain=LMG 31837", "accession": "GCA_905220975.1", "taxid": 2793077, "species_taxid": 2793077, "relation_to_type": "type", "validated": true, "ani": 89.3265, "matched_fragments": 1858, "total_fragments": 2962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia nemoris", "strain": "strain=LMG 31836", "accession": "GCA_905221015.1", "taxid": 2793076, "species_taxid": 2793076, "relation_to_type": "type", "validated": true, "ani": 89.194, "matched_fragments": 1938, "total_fragments": 2962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia solitsugae", "strain": "strain=1N", "accession": "GCA_013177695.1", "taxid": 2675748, "species_taxid": 2675748, "relation_to_type": "type", "validated": true, "ani": 89.105, "matched_fragments": 1857, "total_fragments": 2962, "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": 89.0695, "matched_fragments": 1896, "total_fragments": 2962, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraburkholderia caffeinilytica", "strain": "strain=CF1", "accession": "GCA_003368325.1", "taxid": 1761016, "species_taxid": 1761016, "relation_to_type": "type", "validated": true, "ani": 88.9957, "matched_fragments": 1792, "total_fragments": 2962, "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": 84.012, "matched_fragments": 1222, "total_fragments": 2962, "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": 83.6448, "matched_fragments": 1409, "total_fragments": 2962, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_902833645.1", "gtdb_species": "s__Paraburkholderia fungorum", "ani": 100.0, "matched_fragments": 2961, "total_fragments": 2962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.75", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_003610895.1", "gtdb_species": "s__Paraburkholderia fungorum_B", "ani": 90.4957, "matched_fragments": 2095, "total_fragments": 2962, "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_013177735.1", "gtdb_species": "s__Paraburkholderia sp013177735", "ani": 89.7697, "matched_fragments": 1799, "total_fragments": 2962, "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_012927345.1", "gtdb_species": "s__Paraburkholderia sp012927345", "ani": 89.664, "matched_fragments": 1967, "total_fragments": 2962, "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_001634365.1", "gtdb_species": "s__Paraburkholderia sp001634365", "ani": 89.5479, "matched_fragments": 1577, "total_fragments": 2962, "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_905220975.1", "gtdb_species": "s__Paraburkholderia sp905220975", "ani": 89.3217, "matched_fragments": 1858, "total_fragments": 2962, "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_009690905.1", "gtdb_species": "s__Paraburkholderia madseniana", "ani": 89.2932, "matched_fragments": 1909, "total_fragments": 2962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "98.82", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900116445.1", "gtdb_species": "s__Paraburkholderia aspalathi", "ani": 89.2791, "matched_fragments": 1977, "total_fragments": 2962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.47", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.72", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_003610295.1", "gtdb_species": "s__Paraburkholderia sp003610295", "ani": 89.2717, "matched_fragments": 1910, "total_fragments": 2962, "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_900230185.1", "gtdb_species": "s__Paraburkholderia sp900230185", "ani": 89.2446, "matched_fragments": 2025, "total_fragments": 2962, "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_900142905.1", "gtdb_species": "s__Paraburkholderia sp900142905", "ani": 89.1632, "matched_fragments": 2004, "total_fragments": 2962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.29", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.82", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_013177695.1", "gtdb_species": "s__Paraburkholderia sp013177695", "ani": 89.0924, "matched_fragments": 1861, "total_fragments": 2962, "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_905220835.1", "gtdb_species": "s__Paraburkholderia sp905220835", "ani": 89.035, "matched_fragments": 1889, "total_fragments": 2962, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "99.56", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_003368325.1", "gtdb_species": "s__Paraburkholderia caffeinilytica", "ani": 88.9997, "matched_fragments": 1791, "total_fragments": 2962, "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": 3, "status": "-" }, { "accession": "GCF_003353175.1", "gtdb_species": "s__Paraburkholderia lacunae", "ani": 86.4593, "matched_fragments": 1604, "total_fragments": 2962, "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": 8858424.833, "gc_content": 61.785, "coding_genes": 8037.0, "rRNA16S_genes": 6.0, "tRNA_genes": 64.0, "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", "fungorum" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }