{ "type": "genome", "identifier": "GCF_023347575.1", "organism": "Brenneria tiliae", "title": "Brenneria tiliae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of the West of England", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023347575.1", "bioproject": "PRJNA224116", "biosample": "SAMN25749586", "wgs_master": "JAKPCB000000000.1", "refseq_category": "reference genome", "taxid": "2914984", "species_taxid": "2914984", "organism_name": "Brenneria tiliae", "infraspecific_name": "strain=WC1b.1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/05/12", "asm_name": "ASM2334757v1", "asm_submitter": "University of the West of England", "gbrs_paired_asm": "GCA_023347575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/347/575/GCF_023347575.1_ASM2334757v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5161293", "genome_size_ungapped": "5161293", "gc_percent": "56.500000", "replicon_count": "0", "scaffold_count": "103", "contig_count": "103", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023347575.1-RS_2024_08_04", "annotation_date": "2024-08-04", "total_gene_count": "4801", "protein_coding_gene_count": "4563", "non_coding_gene_count": "135", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-05-12", "dateModified": "2022-05-12", "datePublished": "2022-05-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Brenneria tiliae" ], "sample_taxid": [ "2914984" ], "sample_host_organism": [ "Tilia x moltkei" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: Westonbirt Arboretum" ], "sample_host_location_id": [], "data_size": "1.455 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)": "5161293", "Number of Sequences": "103", "Longest Sequences (bp)": "668036", "N50 (bp)": "273546", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.5", "Number of CDSs": "4659", "Average Protein Length": "321.5", "Coding Ratio (%)": "87.1", "Number of rRNAs": "3", "Number of tRNAs": "76", "Number of CRISPRs": "2" }, "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": 94.9595, "matched_fragments": 1242, "total_fragments": 1699, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria nigrifluens", "strain": "strain=ATCC 13028", "accession": "GCA_005484965.1", "taxid": 55210, "species_taxid": 55210, "relation_to_type": "type", "validated": true, "ani": 94.8941, "matched_fragments": 1276, "total_fragments": 1699, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brenneria alni", "strain": "strain=NCPPB 3934", "accession": "GCA_003666245.1", "taxid": 71656, "species_taxid": 71656, "relation_to_type": "type", "validated": true, "ani": 84.3577, "matched_fragments": 917, "total_fragments": 1699, "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": 83.8561, "matched_fragments": 1082, "total_fragments": 1699, "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": 83.7568, "matched_fragments": 1040, "total_fragments": 1699, "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": 83.7554, "matched_fragments": 1064, "total_fragments": 1699, "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": 82.0948, "matched_fragments": 945, "total_fragments": 1699, "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": 81.9934, "matched_fragments": 943, "total_fragments": 1699, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium quasiaquaticum", "strain": "strain=A477-S1-J17", "accession": "GCA_014946775.2", "taxid": 2774015, "species_taxid": 2774015, "relation_to_type": "type", "validated": true, "ani": 80.5532, "matched_fragments": 708, "total_fragments": 1699, "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": 80.541, "matched_fragments": 730, "total_fragments": 1699, "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": 79.5557, "matched_fragments": 613, "total_fragments": 1699, "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": 79.5494, "matched_fragments": 565, "total_fragments": 1699, "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": 79.4642, "matched_fragments": 593, "total_fragments": 1699, "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": 94.8941, "matched_fragments": 1276, "total_fragments": 1699, "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": "-" }, { "accession": "GCF_013155275.1", "gtdb_species": "s__Brenneria sp013155275", "ani": 85.3425, "matched_fragments": 1066, "total_fragments": 1699, "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": 84.3579, "matched_fragments": 917, "total_fragments": 1699, "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": 83.8445, "matched_fragments": 1082, "total_fragments": 1699, "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": 83.7663, "matched_fragments": 1064, "total_fragments": 1699, "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": 82.1025, "matched_fragments": 944, "total_fragments": 1699, "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_008710095.1", "gtdb_species": "s__Affinibrenneria salicis", "ani": 80.5567, "matched_fragments": 787, "total_fragments": 1699, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Affinibrenneria", "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": -0.199, "cell_length": 0.087, "doubling_h": null, "growth_tmp": 29.8, "optimum_tmp": 25.0, "optimum_ph": null, "genome_size": 4580137.25, "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": 0.2, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.8, "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", "tiliae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }