{ "type": "genome", "identifier": "GCF_000757625.1", "organism": "Pectobacterium parmentieri", "title": "Pectobacterium parmentieri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CNRS - UPR2355", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000757625.1", "bioproject": "PRJNA224116", "biosample": "SAMN02729843", "wgs_master": "JMDL00000000.1", "refseq_category": "na", "taxid": "1905730", "species_taxid": "1905730", "organism_name": "Pectobacterium parmentieri", "infraspecific_name": "strain=RNS 08-42-1A", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/10/03", "asm_name": "PecWasRNS_1.0", "asm_submitter": "CNRS - UPR2355", "gbrs_paired_asm": "GCA_000757625.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/757/625/GCF_000757625.1_PecWasRNS_1.0", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5015359", "genome_size_ungapped": "4980198", "gc_percent": "50.500000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "26", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000757625.1-RS_2024_03_15", "annotation_date": "2024-03-15", "total_gene_count": "4622", "protein_coding_gene_count": "4414", "non_coding_gene_count": "100", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-10-03", "dateModified": "2014-10-03", "datePublished": "2014-10-03", "_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": "1.418 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)": "5015359", "Number of Sequences": "8", "Longest Sequences (bp)": "3310642", "N50 (bp)": "3310642", "Gap Ratio (%)": "0.701066", "GCcontent (%)": "50.4", "Number of CDSs": "4518", "Average Protein Length": "310.7", "Coding Ratio (%)": "84.0", "Number of rRNAs": "17", "Number of tRNAs": "73", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 99.9919, "matched_fragments": 1660, "total_fragments": 1668, "ani_threshold": 95, "status": "conclusive" }, { "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": 99.9783, "matched_fragments": 1659, "total_fragments": 1668, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium wasabiae", "strain": "strain=CFBP 3304", "accession": "GCA_000291725.1", "taxid": 55208, "species_taxid": 55208, "relation_to_type": "type", "validated": true, "ani": 94.008, "matched_fragments": 1444, "total_fragments": 1668, "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", "validated": true, "ani": 94.0028, "matched_fragments": 1462, "total_fragments": 1668, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium wasabiae", "strain": "strain=NCPPB 3701", "accession": "GCA_000749865.1", "taxid": 55208, "species_taxid": 55208, "relation_to_type": "type", "validated": true, "ani": 93.9972, "matched_fragments": 1445, "total_fragments": 1668, "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": 88.6046, "matched_fragments": 1208, "total_fragments": 1668, "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": 88.0655, "matched_fragments": 1258, "total_fragments": 1668, "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": 78.6897, "matched_fragments": 402, "total_fragments": 1668, "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": 78.6652, "matched_fragments": 395, "total_fragments": 1668, "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": 78.3095, "matched_fragments": 322, "total_fragments": 1668, "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": 99.9783, "matched_fragments": 1659, "total_fragments": 1668, "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": 93.9953, "matched_fragments": 1463, "total_fragments": 1668, "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", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_012427845.1", "gtdb_species": "s__Pectobacterium punjabense", "ani": 91.4601, "matched_fragments": 1326, "total_fragments": 1668, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_005497185.1", "gtdb_species": "s__Pectobacterium polonicum", "ani": 91.1121, "matched_fragments": 1313, "total_fragments": 1668, "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_002847345.1", "gtdb_species": "s__Pectobacterium peruviense", "ani": 89.9773, "matched_fragments": 1284, "total_fragments": 1668, "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": 89.8977, "matched_fragments": 1282, "total_fragments": 1668, "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", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 14, "status": "-" }, { 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"accession": "GCF_000754695.1", "gtdb_species": "s__Pectobacterium brasiliense", "ani": 88.8291, "matched_fragments": 1287, "total_fragments": 1668, "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, "range_salinity": 0.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, 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