{ "type": "genome", "identifier": "GCF_001742145.1", "organism": "Pectobacterium parmentieri", "title": "Pectobacterium parmentieri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute for integrative biology of the cell", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001742145.1", "bioproject": "PRJNA224116", "biosample": "SAMN02729843", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1905730", "species_taxid": "1905730", "organism_name": "Pectobacterium parmentieri", "infraspecific_name": "strain=RNS 08-42-1A", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/09/22", "asm_name": "ASM174214v1", "asm_submitter": "Institute for integrative biology of the cell", "gbrs_paired_asm": "GCA_001742145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/742/145/GCF_001742145.1_ASM174214v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5030841", "genome_size_ungapped": "5030841", "gc_percent": "50.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-04", "total_gene_count": "4661", "protein_coding_gene_count": "4454", "non_coding_gene_count": "107", "pubmed_id": "27692046;25297844" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-09-22", "dateModified": "2016-09-22", "datePublished": "2016-09-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Pectobacterium parmentieri" ], "sample_taxid": [ "1905730" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "1.427 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)": "5030841", "Number of Sequences": "1", "Longest Sequences (bp)": "5030841", "N50 (bp)": "5030841", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.4", "Number of CDSs": "4569", "Average Protein Length": "311.0", "Coding Ratio (%)": "84.7", "Number of rRNAs": "22", "Number of tRNAs": "77", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pectobacterium parmentieri", "strain": "strain=RNS 08-42-1A", "accession": "GCA_001742145.1", "taxid": 1905730, "species_taxid": 1905730, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1676, "total_fragments": 1676, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium parmentieri", "strain": "strain=RNS 08-42-1A", "accession": "GCA_000757625.1", "taxid": 1905730, "species_taxid": 1905730, "relation_to_type": "type", "validated": true, "ani": 99.9729, "matched_fragments": 1655, "total_fragments": 1676, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium wasabiae", "strain": "strain=NCPPB 3701", "accession": "GCA_000749865.1", "taxid": 55208, "species_taxid": 55208, "relation_to_type": "type", "validated": true, "ani": 93.9982, "matched_fragments": 1445, "total_fragments": 1676, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium wasabiae", "strain": "strain=CFBP 3304", "accession": "GCA_001742185.1", "taxid": 55208, "species_taxid": 55208, "relation_to_type": "type", 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"matched_fragments": 1242, "total_fragments": 1676, "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": 78.7879, "matched_fragments": 400, "total_fragments": 1676, "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": 78.6233, "matched_fragments": 397, "total_fragments": 1676, "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": 78.3658, "matched_fragments": 319, "total_fragments": 1676, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001742145.1", "gtdb_species": "s__Pectobacterium parmentieri", "ani": 100.0, "matched_fragments": 1676, "total_fragments": 1676, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 33, "status": "conclusive" }, { "accession": "GCF_001742185.1", "gtdb_species": "s__Pectobacterium wasabiae", "ani": 93.9644, "matched_fragments": 1469, "total_fragments": 1676, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", 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"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_002847345.1", "gtdb_species": "s__Pectobacterium peruviense", "ani": 89.8969, "matched_fragments": 1295, "total_fragments": 1676, "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": "-" }, { "accession": "GCF_019056595.1", "gtdb_species": "s__Pectobacterium atrosepticum", "ani": 89.8448, "matched_fragments": 1297, "total_fragments": 1676, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", 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"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_000754695.1", "gtdb_species": "s__Pectobacterium brasiliense", "ani": 88.7745, "matched_fragments": 1267, "total_fragments": 1676, "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": "-" } ] }, "_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": 5047892.5, "gc_content": 50.48, "coding_genes": 4433.2, "rRNA16S_genes": 7.0, "tRNA_genes": 76.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, 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