{ "type": "genome", "identifier": "GCF_014644155.1", "organism": "Pseudoduganella buxea", "title": "Pseudoduganella buxea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014644155.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245098", "wgs_master": "BMKG00000000.1", "refseq_category": "reference genome", "taxid": "1949069", "species_taxid": "1949069", "organism_name": "Pseudoduganella buxea", "infraspecific_name": "strain=CGMCC 1.15931", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1464415v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014644155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/644/155/GCF_014644155.1_ASM1464415v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6335967", "genome_size_ungapped": "6335841", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "77", "contig_count": "77", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014644155.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "5516", "protein_coding_gene_count": "5375", "non_coding_gene_count": "86", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoduganella buxea" ], "sample_taxid": [ "1949069" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.733 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)": "6335967", "Number of Sequences": "77", "Longest Sequences (bp)": "603896", "N50 (bp)": "230068", "Gap Ratio (%)": "0.002052", "GCcontent (%)": "66.0", "Number of CDSs": "5383", "Average Protein Length": "351.9", "Coding Ratio (%)": "89.7", "Number of rRNAs": "7", "Number of tRNAs": "81", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoduganella buxea", "strain": "strain=CGMCC 1.15931", "accession": "GCA_014644155.1", "taxid": 1949069, "species_taxid": 1949069, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2070, "total_fragments": 2075, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoduganella buxea", "strain": "strain=KCTC 52429", "accession": "GCA_009720835.1", "taxid": 1949069, "species_taxid": 1949069, "relation_to_type": "type", "validated": true, "ani": 99.9467, "matched_fragments": 1968, "total_fragments": 2075, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoduganella armeniaca", "strain": "strain=ZMN-3", "accession": "GCA_003028855.1", "taxid": 2072590, "species_taxid": 2072590, "relation_to_type": "type", "validated": true, "ani": 86.1676, "matched_fragments": 1571, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella plicata", "strain": "strain=KCTC 12344", "accession": "GCA_014651435.1", "taxid": 321984, "species_taxid": 321984, "relation_to_type": "type", "validated": true, "ani": 85.4775, "matched_fragments": 1512, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella plicata", "strain": "strain=DSM 17505", "accession": "GCA_004421005.1", "taxid": 321984, "species_taxid": 321984, "relation_to_type": "type", "validated": true, "ani": 85.4726, "matched_fragments": 1525, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella lurida", "strain": "strain=CGMCC 1.10822", "accession": "GCA_007830455.1", "taxid": 1036180, "species_taxid": 1036180, "relation_to_type": "type", "validated": true, "ani": 83.9736, "matched_fragments": 1288, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella albidiflava", "strain": "strain=DSM 17472", "accession": "GCA_004322755.1", "taxid": 321983, "species_taxid": 321983, "relation_to_type": "type", "validated": true, "ani": 83.3408, "matched_fragments": 1437, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella albidiflava", "strain": "strain=KCTC 12343", "accession": "GCA_014651415.1", "taxid": 321983, "species_taxid": 321983, "relation_to_type": "type", "validated": true, "ani": 83.301, "matched_fragments": 1434, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella lutea", "strain": "strain=DSM 17473", "accession": "GCA_004209755.1", "taxid": 321985, "species_taxid": 321985, "relation_to_type": "type", "validated": true, "ani": 82.9977, "matched_fragments": 1379, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella namucuonensis", "strain": "strain=CGMCC 1.11014", "accession": "GCA_900116645.1", "taxid": 1035707, "species_taxid": 1035707, "relation_to_type": "type", "validated": true, "ani": 82.1334, "matched_fragments": 1235, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella aquatica", "strain": "strain=FT127W", "accession": "GCA_009857595.1", "taxid": 2660641, "species_taxid": 2660641, "relation_to_type": "type", "validated": true, "ani": 81.8233, "matched_fragments": 1181, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella guangdongensis", "strain": "strain=DS3", "accession": "GCA_009857475.1", "taxid": 2692179, "species_taxid": 2692179, "relation_to_type": "type", "validated": true, "ani": 81.1388, "matched_fragments": 1061, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia cavernae", "strain": "strain=K1S02-61", "accession": "GCA_003590855.1", "taxid": 2320864, "species_taxid": 2320864, "relation_to_type": "type", "validated": true, "ani": 80.6953, "matched_fragments": 817, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia agri", "strain": "strain=JCM 31661", "accession": "GCA_024753255.1", "taxid": 1886785, "species_taxid": 1886785, "relation_to_type": "type", "validated": true, "ani": 80.6574, "matched_fragments": 978, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia terrae", "strain": "strain=JCM 31606", "accession": "GCA_024753145.1", "taxid": 1811224, "species_taxid": 1811224, "relation_to_type": "type", "validated": true, "ani": 80.6072, "matched_fragments": 882, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia forsythiae", "strain": "strain=GN2-R2", "accession": "GCA_012849555.1", "taxid": 2728020, "species_taxid": 2728020, "relation_to_type": "type", "validated": true, "ani": 80.4559, "matched_fragments": 1027, "total_fragments": 2075, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009720835.1", "gtdb_species": "s__Pseudoduganella buxea", "ani": 99.9467, "matched_fragments": 1968, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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": "conclusive" }, { "accession": "GCA_008011715.1", "gtdb_species": "s__Pseudoduganella haloabium", "ani": 86.2083, "matched_fragments": 1561, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003028855.1", "gtdb_species": "s__Pseudoduganella armeniaca", "ani": 86.1719, "matched_fragments": 1570, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_004421005.1", "gtdb_species": "s__Pseudoduganella plicata", "ani": 85.4751, "matched_fragments": 1524, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002454505.1", "gtdb_species": "s__Pseudoduganella sp002454505", "ani": 84.3049, "matched_fragments": 1229, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_007830455.1", "gtdb_species": "s__Pseudoduganella lurida", "ani": 83.8971, "matched_fragments": 1299, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_009727155.1", "gtdb_species": "s__Pseudoduganella dura", "ani": 83.3699, "matched_fragments": 1376, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004322755.1", "gtdb_species": "s__Pseudoduganella albidiflava", "ani": 83.3464, "matched_fragments": 1435, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_004209755.1", "gtdb_species": "s__Pseudoduganella lutea", "ani": 82.9739, "matched_fragments": 1384, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_900116645.1", "gtdb_species": "s__Pseudoduganella namucuonensis", "ani": 82.1589, "matched_fragments": 1232, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_003053665.1", "gtdb_species": "s__Pseudoduganella sp003053665", "ani": 82.1245, "matched_fragments": 1227, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "95.97", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001191005.1", "gtdb_species": "s__Pseudoduganella sp001191005", "ani": 81.9709, "matched_fragments": 1094, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_013369485.1", "gtdb_species": "s__Pseudoduganella sp013369485", "ani": 81.7989, "matched_fragments": 1073, "total_fragments": 2075, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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": -0.097, "doubling_h": null, "growth_tmp": 28.5, "optimum_tmp": 29.0, "optimum_ph": null, "genome_size": 6107837.0, "gc_content": 63.0, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "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": [ "Pseudoduganella", "buxea" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }