{ "type": "genome", "identifier": "GCF_026800125.1", "organism": "Pectobacterium jejuense", "title": "Pectobacterium jejuense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyungpook National University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_026800125.1", "bioproject": "PRJNA224116", "biosample": "SAMN30435626", "wgs_master": "JAPQKX000000000.1", "refseq_category": "reference genome", "taxid": "2974022", "species_taxid": "2974022", "organism_name": "Pectobacterium jejuense", "infraspecific_name": "strain=13-115", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/12/10", "asm_name": "ASM2680012v1", "asm_submitter": "Kyungpook National University", "gbrs_paired_asm": "GCA_026800125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/026/800/125/GCF_026800125.1_ASM2680012v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5069478", "genome_size_ungapped": "5069478", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "73", "contig_count": "73", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_026800125.1-RS_2024_08_19", "annotation_date": "2024-08-19", "total_gene_count": "4506", "protein_coding_gene_count": "4360", "non_coding_gene_count": "83", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-12-10", "dateModified": "2022-12-10", "datePublished": "2022-12-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Pectobacterium jejuense" ], "sample_taxid": [ "2974022" ], "sample_host_organism": [ "Cucumis sativus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jeju island" ], "sample_host_location_id": [], "data_size": "1.443 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)": "5069478", "Number of Sequences": "73", "Longest Sequences (bp)": "785270", "N50 (bp)": "408756", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.0", "Number of CDSs": "4404", "Average Protein Length": "324.8", "Coding Ratio (%)": "84.7", "Number of rRNAs": "2", "Number of tRNAs": "70", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pectobacterium brasiliense", "strain": "strain=LMG 21371", "accession": "GCA_000754695.1", "taxid": 180957, "species_taxid": 180957, "relation_to_type": "type", "validated": true, "ani": 94.6218, "matched_fragments": 1392, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "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": 94.6202, "matched_fragments": 1418, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium carotovorum subsp. carotovorum", "strain": "strain=NCPPB 312", "accession": "GCA_000749855.1", "taxid": 555, "species_taxid": 554, "relation_to_type": "suspected-type", "validated": true, "ani": 93.6956, "matched_fragments": 1394, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium carotovorum subsp. carotovorum", "strain": "strain=ICMP 5702", "accession": "GCA_001039055.1", "taxid": 555, "species_taxid": 554, "relation_to_type": "suspected-type", "validated": true, "ani": 93.6933, "matched_fragments": 1397, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium carotovorum", "strain": "strain=DSM 30168", "accession": "GCA_900129615.1", "taxid": 554, "species_taxid": 554, "relation_to_type": "type", "validated": true, "ani": 93.6774, "matched_fragments": 1401, "total_fragments": 1666, "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": 93.3772, "matched_fragments": 1251, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium versatile", "strain": "strain=CFBP6051", "accession": "GCA_004296685.1", "taxid": 2488639, "species_taxid": 2488639, "relation_to_type": "type", "validated": true, "ani": 93.3556, "matched_fragments": 1399, "total_fragments": 1666, "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": 90.6357, "matched_fragments": 1331, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium atrosepticum", "strain": "strain=ICMP 1526", "accession": "GCA_001038685.1", "taxid": 29471, "species_taxid": 29471, "relation_to_type": "type", "validated": true, "ani": 89.6604, "matched_fragments": 1302, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella ecdela", "strain": "strain=FRB 231", "accession": "GCA_019049625.1", "taxid": 2816250, "species_taxid": 2816250, "relation_to_type": "type", "validated": true, "ani": 78.3978, "matched_fragments": 421, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella bonaserana", "strain": "strain=H11b", "accession": "GCA_019049675.1", "taxid": 2816248, "species_taxid": 2816248, "relation_to_type": "type", "validated": true, "ani": 78.3907, "matched_fragments": 417, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 78.3032, "matched_fragments": 392, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Proteus mirabilis", "strain": "strain=ATCC 29906", "accession": "GCA_000160755.1", "taxid": 584, "species_taxid": 584, "relation_to_type": "type", "validated": true, "ani": 77.8394, "matched_fragments": 85, "total_fragments": 1666, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002307355.1", "gtdb_species": "s__Pectobacterium polaris", "ani": 95.0864, "matched_fragments": 1412, "total_fragments": 1666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 21, "status": "conclusive" }, { "accession": "GCF_000754695.1", "gtdb_species": "s__Pectobacterium brasiliense", "ani": 94.601, "matched_fragments": 1394, "total_fragments": 1666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.37", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 92, "status": "-" }, { "accession": "GCF_013449685.1", "gtdb_species": "s__Pectobacterium brasiliense_A", "ani": 93.8764, "matched_fragments": 1258, "total_fragments": 1666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "96.08", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_900129615.1", "gtdb_species": "s__Pectobacterium carotovorum", "ani": 93.6774, "matched_fragments": 1401, "total_fragments": 1666, "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", 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"min_intra_species_ani": "98.49", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013449375.1", "gtdb_species": "s__Pectobacterium sp013449375", "ani": 90.8151, "matched_fragments": 1244, "total_fragments": 1666, "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": "GCF_015689195.1", "gtdb_species": "s__Pectobacterium aroidearum", "ani": 90.787, "matched_fragments": 1390, "total_fragments": 1666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", 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"min_intra_species_ani": "98.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_002847345.1", "gtdb_species": "s__Pectobacterium peruviense", "ani": 89.7108, "matched_fragments": 1369, "total_fragments": 1666, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "97.64", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "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, 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