{ "type": "genome", "identifier": "GCF_016950255.1", "organism": "Pectobacterium brasiliense", "title": "Pectobacterium brasiliense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Wageningen Plant Research", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016950255.1", "bioproject": "PRJNA224116", "biosample": "SAMN15660329", "wgs_master": "JACGFN000000000.1", "refseq_category": "na", "taxid": "180957", "species_taxid": "180957", "organism_name": "Pectobacterium brasiliense", "infraspecific_name": "strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/25", "asm_name": "ASM1695025v1", "asm_submitter": "Wageningen Plant Research", "gbrs_paired_asm": "GCA_016950255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/950/255/GCF_016950255.1_ASM1695025v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4880585", "genome_size_ungapped": "4880585", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016950255.1-RS_2024_04_02", "annotation_date": "2024-04-02", "total_gene_count": "4360", "protein_coding_gene_count": "4155", "non_coding_gene_count": "113", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-25", "dateModified": "2021-02-25", "datePublished": "2021-02-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Pectobacterium brasiliense" ], "sample_taxid": [ "180957" ], "sample_host_organism": [ "Solanum tuberosum cv. Elvira" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Rio Grande do Sul, Planalto" ], "sample_host_location_id": [], "data_size": "1.383 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)": "4880585", "Number of Sequences": "7", "Longest Sequences (bp)": "3291298", "N50 (bp)": "3291298", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.2", "Number of CDSs": "4289", "Average Protein Length": "326.7", "Coding Ratio (%)": "86.1", "Number of rRNAs": "24", "Number of tRNAs": "80", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pectobacterium brasiliense", "strain": "strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692", "accession": "GCA_016950255.1", "taxid": 180957, "species_taxid": 180957, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1624, "total_fragments": 1624, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium brasiliense", "strain": "strain=LMG 21371", "accession": "GCA_000754695.1", "taxid": 180957, "species_taxid": 180957, "relation_to_type": "type", "validated": true, "ani": 99.9869, "matched_fragments": 1575, "total_fragments": 1624, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium polaris", "strain": "strain=NIBIO1006", "accession": "GCA_002307355.1", "taxid": 2042057, "species_taxid": 2042057, "relation_to_type": "type", "validated": true, "ani": 94.067, "matched_fragments": 1379, "total_fragments": 1624, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium quasiaquaticum", "strain": "strain=A477-S1-J17", "accession": "GCA_014946775.2", "taxid": 2774015, 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"95.13", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_900129615.1", "gtdb_species": "s__Pectobacterium carotovorum", "ani": 93.3147, "matched_fragments": 1361, "total_fragments": 1624, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.11", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 81, "status": "-" }, { "accession": "GCF_003382565.2", "gtdb_species": "s__Pectobacterium aquaticum", "ani": 93.0205, "matched_fragments": 1172, "total_fragments": 1624, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.07", "min_intra_species_ani": 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"97.92", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_013449375.1", "gtdb_species": "s__Pectobacterium sp013449375", "ani": 90.8575, "matched_fragments": 1257, "total_fragments": 1624, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "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": "GCA_000010085.1", "gtdb_species": "s__Sodalis glossinidius", "ani": 78.0724, "matched_fragments": 208, "total_fragments": 1624, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.104, "growth_tmp": 27.416, "optimum_tmp": 29.406, "optimum_ph": 6.25, "genome_size": 4916069.627, "gc_content": 50.885, "coding_genes": 4336.072, "rRNA16S_genes": 7.0, "tRNA_genes": 76.833, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.714, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.285, "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": [ "Pectobacterium", "brasiliense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }