{ "type": "genome", "identifier": "GCF_003096595.1", "organism": "Pusillimonas noertemannii", "title": "Pusillimonas noertemannii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003096595.1", "bioproject": "PRJNA224116", "biosample": "SAMN08770177", "wgs_master": "QEKO00000000.1", "refseq_category": "na", "taxid": "305977", "species_taxid": "305977", "organism_name": "Pusillimonas noertemannii", "infraspecific_name": "strain=DSM 10065", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/07", "asm_name": "ASM309659v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003096595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/096/595/GCF_003096595.1_ASM309659v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4203487", "genome_size_ungapped": "4203199", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "15", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003096595.1-RS_2024_04_15", "annotation_date": "2024-04-15", "total_gene_count": "3948", "protein_coding_gene_count": "3868", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-07", "dateModified": "2018-05-07", "datePublished": "2018-05-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Pusillimonas noertemannii" ], "sample_taxid": [ "305977" ], "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": "1.174 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)": "4203487", "Number of Sequences": "15", "Longest Sequences (bp)": "1467833", "N50 (bp)": "847891", "Gap Ratio (%)": "0.006851", "GCcontent (%)": "62.6", "Number of CDSs": "3875", "Average Protein Length": "326.5", "Coding Ratio (%)": "90.3", "Number of rRNAs": "3", "Number of tRNAs": "44", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pusillimonas noertemannii", "strain": "strain=DSM 10065", "accession": "GCA_003096595.1", "taxid": 305977, "species_taxid": 305977, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1390, "total_fragments": 1393, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pusillimonas noertemannii", "strain": "strain=DSM 10065", "accession": "GCA_003545825.1", "taxid": 305977, "species_taxid": 305977, "relation_to_type": "type", "validated": true, "ani": 99.9996, "matched_fragments": 1393, "total_fragments": 1393, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pusillimonas noertemannii", "strain": "strain=DSM 10065", "accession": "GCA_013416295.1", "taxid": 305977, "species_taxid": 305977, "relation_to_type": "type", "validated": true, "ani": 99.9979, "matched_fragments": 1388, "total_fragments": 1393, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pusillimonas caeni", "strain": "strain=KCTC 42353", "accession": "GCA_003545815.1", "taxid": 1348472, "species_taxid": 1348472, "relation_to_type": "type", "validated": true, "ani": 86.6811, "matched_fragments": 1018, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parapusillimonas granuli", "strain": "strain=LMG 24012", "accession": "GCA_013416525.1", "taxid": 380911, "species_taxid": 380911, "relation_to_type": "type", "validated": true, "ani": 79.8268, "matched_fragments": 468, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Candidimonas nitroreducens", "strain": "strain=SC-089", "accession": "GCA_002209565.1", "taxid": 683354, "species_taxid": 683354, "relation_to_type": "type", "validated": true, "ani": 79.7888, "matched_fragments": 484, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Candidimonas humi", "strain": "strain=DSM 25336", "accession": "GCA_019166065.1", "taxid": 683355, "species_taxid": 683355, "relation_to_type": "type", "validated": true, "ani": 79.6449, "matched_fragments": 451, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Eoetvoesia caeni", "strain": "strain=PB3-7B", "accession": "GCA_022688825.1", "taxid": 645616, "species_taxid": 645616, "relation_to_type": "type", "validated": true, "ani": 79.2284, "matched_fragments": 507, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella pertussis", "strain": "strain=18323", "accession": "GCA_000306945.1", "taxid": 520, "species_taxid": 520, "relation_to_type": "type", "validated": true, "ani": 79.1641, "matched_fragments": 409, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella bronchiseptica", "strain": "strain=CCUG 219", "accession": "GCA_021391275.1", "taxid": 518, "species_taxid": 518, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0446, "matched_fragments": 424, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter xylosoxidans", "strain": "strain=PartM-Axylosoxidans-RM8376", "accession": "GCA_022870085.1", "taxid": 85698, "species_taxid": 85698, "relation_to_type": "type", "validated": true, "ani": 79.0241, "matched_fragments": 451, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella pseudohinzii", "strain": "strain=8-296-03", "accession": "GCA_000657795.2", "taxid": 1331258, "species_taxid": 1331258, "relation_to_type": "type", "validated": true, "ani": 78.8908, "matched_fragments": 410, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter insolitus", "strain": "strain=NCTC 13520", "accession": "GCA_024168865.1", "taxid": 217204, "species_taxid": 217204, "relation_to_type": "type", "validated": true, "ani": 78.5219, "matched_fragments": 379, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ralstonia pseudosolanacearum", "strain": "strain=LMG 9673", "accession": "GCA_919586305.1", "taxid": 1310165, "species_taxid": 1310165, "relation_to_type": "type", "validated": true, "ani": 77.1887, "matched_fragments": 232, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thauera humireducens", "strain": "strain=SgZ-1", "accession": "GCA_001051995.2", "taxid": 1134435, "species_taxid": 1134435, "relation_to_type": "type", "validated": true, "ani": 76.6646, "matched_fragments": 159, "total_fragments": 1393, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003096595.1", "gtdb_species": "s__Pusillimonas noertemannii", "ani": 100.0, "matched_fragments": 1390, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.25", "min_intra_species_ani": "97.76", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_003545815.1", "gtdb_species": "s__Pusillimonas caeni", "ani": 86.6575, "matched_fragments": 1020, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas", "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_013416525.1", "gtdb_species": "s__Parapusillimonas granuli", "ani": 79.8499, "matched_fragments": 466, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002209565.1", "gtdb_species": "s__Candidimonas nitroreducens", "ani": 79.7889, "matched_fragments": 484, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas", "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_019166065.1", "gtdb_species": "s__Candidimonas humi", "ani": 79.6675, "matched_fragments": 450, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas", "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_017356245.1", "gtdb_species": "s__Bordetella_A petrii_D", "ani": 79.4117, "matched_fragments": 457, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A", "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_017745595.1", "gtdb_species": "s__Bordetella_A petrii_C", "ani": 79.408, "matched_fragments": 469, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A", "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_002261345.1", "gtdb_species": "s__Bordetella_A sp002261345", "ani": 79.325, "matched_fragments": 437, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_013416435.1", "gtdb_species": "s__Parapusillimonas sp013416435", "ani": 79.3138, "matched_fragments": 399, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas", "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_001270295.1", "gtdb_species": "s__Achromobacter sp001270295", "ani": 79.1924, "matched_fragments": 387, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter", "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_900129885.1", "gtdb_species": "s__Candidimonas_A bauzanensis", "ani": 79.1032, "matched_fragments": 455, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A", "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_002261225.1", "gtdb_species": "s__Bordetella_C sp002261225", "ani": 78.767, "matched_fragments": 416, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C", "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_002261265.1", "gtdb_species": "s__Bordetella_A sp002261265", "ani": 78.7383, "matched_fragments": 382, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002188635.1", "gtdb_species": "s__Pigmentiphaga sp002188635", "ani": 78.0527, "matched_fragments": 396, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_001577345.1", "gtdb_species": "s__Gallionella acididurans", "ani": 76.8062, "matched_fragments": 57, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella", "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_001051995.2", "gtdb_species": "s__Thauera humireducens", "ani": 76.6524, "matched_fragments": 160, "total_fragments": 1393, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.188, "cell_length": 0.096, "doubling_h": null, "growth_tmp": 32.0, "optimum_tmp": 30.0, "optimum_ph": 7.2, "genome_size": 4060232.0, "gc_content": null, "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": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Pusillimonas", "noertemannii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }