{ "type": "genome", "identifier": "GCF_003115835.1", "organism": "Brenneria nigrifluens DSM 30175 = ATCC 13028", "title": "Brenneria nigrifluens DSM 30175 = ATCC 13028", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Institute of Forest Ecology Environment and Protection", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003115835.1", "bioproject": "PRJNA224116", "biosample": "SAMN06481725", "wgs_master": "QDKK00000000.1", "refseq_category": "na", "taxid": "1121120", "species_taxid": "55210", "organism_name": "Brenneria nigrifluens DSM 30175 = ATCC 13028", "infraspecific_name": "strain=LMG 2694", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/11", "asm_name": "ASM311583v1", "asm_submitter": "Research Institute of Forest Ecology Environment and Protection", "gbrs_paired_asm": "GCA_003115835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/115/835/GCF_003115835.1_ASM311583v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4844186", "genome_size_ungapped": "4844130", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "77", "contig_count": "102", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003115835.1-RS_2024_05_11", "annotation_date": "2024-05-11", "total_gene_count": "4589", "protein_coding_gene_count": "4385", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-11", "dateModified": "2018-05-11", "datePublished": "2018-05-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Brenneria nigrifluens DSM 30175 = ATCC 13028" ], "sample_taxid": [ "1121120" ], "sample_host_organism": [ "walnut" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.372 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4844186", "Number of Sequences": "77", "Longest Sequences (bp)": "548104", "N50 (bp)": "231722", "Gap Ratio (%)": "0.001156", "GCcontent (%)": "55.9", "Number of CDSs": "4447", "Average Protein Length": "314.0", "Coding Ratio (%)": "86.5", "Number of rRNAs": "2", "Number of tRNAs": "65", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brenneria nigrifluens", "strain": "strain=LMG 2694", "accession": "GCA_003115835.1", "taxid": 55210, "species_taxid": 55210, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1584, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brenneria nigrifluens", "strain": "strain=ATCC 13028", "accession": "GCA_005484965.1", "taxid": 55210, "species_taxid": 55210, "relation_to_type": "type", "validated": true, "ani": 99.9961, "matched_fragments": 1572, "total_fragments": 1584, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brenneria alni", "strain": "strain=NCPPB 3934", "accession": "GCA_003666245.1", "taxid": 71656, "species_taxid": 71656, "relation_to_type": "type", "validated": true, "ani": 84.6244, "matched_fragments": 955, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria izadpanahii", "strain": "strain=Iran 50", "accession": "GCA_017569925.1", "taxid": 2722756, "species_taxid": 2722756, "relation_to_type": "type", "validated": true, "ani": 83.9548, "matched_fragments": 1013, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria goodwinii", "strain": "strain=FRB141", "accession": "GCA_003666235.1", "taxid": 1109412, "species_taxid": 1109412, "relation_to_type": "type", "validated": true, "ani": 83.8707, "matched_fragments": 1018, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria goodwinii", "strain": "strain=FRB141", "accession": "GCA_002291445.1", "taxid": 1109412, "species_taxid": 1109412, "relation_to_type": "type", "validated": true, "ani": 83.7993, "matched_fragments": 1047, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria roseae subsp. americana", "strain": "strain=LMG 27715", "accession": "GCA_003115815.1", "taxid": 1508507, "species_taxid": 1509241, "relation_to_type": "type", "validated": true, "ani": 81.9951, "matched_fragments": 933, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria roseae subsp. roseae", "strain": "strain=LMG 27714", "accession": "GCA_003115845.1", "taxid": 1508506, "species_taxid": 1509241, "relation_to_type": "type", "validated": true, "ani": 81.8022, "matched_fragments": 910, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium colocasium", "strain": "strain=LJ1", "accession": "GCA_020181655.1", "taxid": 2878098, "species_taxid": 2878098, "relation_to_type": "type", "validated": true, "ani": 80.4997, "matched_fragments": 738, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia nevei", "strain": "strain=S15", "accession": "GCA_008364245.1", "taxid": 2703794, "species_taxid": 2703794, "relation_to_type": "type", "validated": true, "ani": 79.4481, "matched_fragments": 547, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia entomophila", "strain": "strain=A1", "accession": "GCA_021462285.1", "taxid": 42906, "species_taxid": 42906, "relation_to_type": "type", "validated": true, "ani": 79.3529, "matched_fragments": 566, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia bockelmannii", "strain": "strain=S3", "accession": "GCA_008011855.1", "taxid": 2703793, "species_taxid": 2703793, "relation_to_type": "type", "validated": true, "ani": 79.3203, "matched_fragments": 538, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Musicola keenii", "strain": "strain=A3967", "accession": "GCA_022761095.1", "taxid": 2884250, "species_taxid": 2884250, "relation_to_type": "type", "validated": true, "ani": 79.0805, "matched_fragments": 531, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter braakii", "strain": "strain=ATCC 51113", "accession": "GCA_002075345.1", "taxid": 57706, "species_taxid": 57706, "relation_to_type": "type", "validated": true, "ani": 78.176, "matched_fragments": 275, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter youngae", "strain": "strain=NCTC13709", "accession": "GCA_900638065.1", "taxid": 133448, "species_taxid": 133448, "relation_to_type": "type", "validated": true, "ani": 78.1239, "matched_fragments": 282, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter youngae", "strain": "strain=CCUG 30791", "accession": "GCA_003818115.1", "taxid": 133448, "species_taxid": 133448, "relation_to_type": "type", "validated": true, "ani": 78.0479, "matched_fragments": 277, "total_fragments": 1584, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.92, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005484965.1", "gtdb_species": "s__Brenneria nigrifluens", "ani": 99.9961, "matched_fragments": 1572, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "95.07", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.76", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_013155275.1", "gtdb_species": "s__Brenneria sp013155275", "ani": 85.1542, "matched_fragments": 1015, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "99.39", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003666245.1", "gtdb_species": "s__Brenneria alni", "ani": 84.618, "matched_fragments": 956, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "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_017569925.1", "gtdb_species": "s__Brenneria izadpanahii", "ani": 83.9403, "matched_fragments": 1015, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "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_002291445.1", "gtdb_species": "s__Brenneria goodwinii", "ani": 83.7796, "matched_fragments": 1049, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.30", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003115845.1", "gtdb_species": "s__Brenneria roseae", "ani": 81.7815, "matched_fragments": 914, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.57", "min_intra_species_ani": "96.57", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005484945.1", "gtdb_species": "s__Brenneria rubrifaciens", "ani": 81.7242, "matched_fragments": 813, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria", "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_015999465.1", "gtdb_species": "s__Lonsdalea populi", "ani": 79.4867, "matched_fragments": 529, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.60", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCF_001976145.1", "gtdb_species": "s__Chania oryzae", "ani": 78.4485, "matched_fragments": 427, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.79", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900094795.1", "gtdb_species": "s__Kosakonia oryziphila", "ani": 77.9172, "matched_fragments": 362, "total_fragments": 1584, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia", "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": 0.113, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 25.0, "optimum_ph": null, "genome_size": 4816511.0, "gc_content": 53.1, "coding_genes": 4563.5, "rRNA16S_genes": 7.0, "tRNA_genes": 75.0, "gram_stain": 0.0, "sporulation": null, "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": [ "Brenneria", "nigrifluens", "DSM", "30175", "=", "ATCC", "13028" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }