{ "type": "genome", "identifier": "GCF_029635795.1", "organism": "Dickeya lacustris", "title": "Dickeya lacustris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Hawaii", "publication": [ {} ], "properties": { "assembly_accession": "GCF_029635795.1", "bioproject": "PRJNA224116", "biosample": "SAMN32157251", "wgs_master": "na", "refseq_category": "na", "taxid": "2259638", "species_taxid": "2259638", "organism_name": "Dickeya lacustris", "infraspecific_name": "strain=LMG30899", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/04/10", "asm_name": "ASM2963579v1", "asm_submitter": "University of Hawaii", "gbrs_paired_asm": "GCA_029635795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/635/795/GCF_029635795.1_ASM2963579v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4367773", "genome_size_ungapped": "4367773", "gc_percent": "53.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_029635795.1-RS_2024_04_10", "annotation_date": "2024-04-10", "total_gene_count": "3945", "protein_coding_gene_count": "3664", "non_coding_gene_count": "104", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-04-10", "dateModified": "2023-04-10", "datePublished": "2023-04-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Dickeya lacustris" ], "sample_taxid": [ "2259638" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Les Dombes" ], "sample_host_location_id": [], "data_size": "1.232 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4367773", "Number of Sequences": "1", "Longest Sequences (bp)": "4367773", "N50 (bp)": "4367773", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.1", "Number of CDSs": "3951", "Average Protein Length": "312.2", "Coding Ratio (%)": "84.7", "Number of rRNAs": "22", "Number of tRNAs": "77", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Dickeya lacustris", "strain": "strain=S29", "accession": "GCA_003934295.1", "taxid": 2259638, "species_taxid": 2259638, "relation_to_type": "type", "validated": true, "ani": 99.9635, "matched_fragments": 1394, "total_fragments": 1455, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Dickeya aquatica", "strain": "strain=174/2", "accession": "GCA_900095885.1", "taxid": 1401087, "species_taxid": 1401087, "relation_to_type": "type", "validated": true, "ani": 89.2234, "matched_fragments": 1250, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya fangzhongdai", "strain": "strain=DSM 101947", "accession": "GCA_002812485.1", "taxid": 1778540, "species_taxid": 1778540, "relation_to_type": "type", "validated": true, "ani": 82.0808, "matched_fragments": 938, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya chrysanthemi", "strain": "strain=NCPPB 402", "accession": "GCA_000406105.1", "taxid": 556, "species_taxid": 556, "relation_to_type": "type", "validated": true, "ani": 82.0416, "matched_fragments": 912, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya poaceiphila", "strain": "strain=NCPPB 569", "accession": "GCA_007858975.2", "taxid": 568768, "species_taxid": 568768, "relation_to_type": "type", "validated": true, "ani": 82.035, "matched_fragments": 844, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya zeae", "strain": "strain=NCPPB 2538", "accession": "GCA_000406165.1", "taxid": 204042, "species_taxid": 204042, "relation_to_type": "type", "validated": true, "ani": 82.015, "matched_fragments": 916, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya dadantii subsp. dieffenbachiae", "strain": "strain=NCPPB 2976", "accession": "GCA_000406185.1", "taxid": 204040, "species_taxid": 204038, "relation_to_type": "type", "validated": true, "ani": 81.9946, "matched_fragments": 925, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya fangzhongdai", "strain": "strain=CGMCC 1.15464", "accession": "GCA_014642955.1", "taxid": 1778540, "species_taxid": 1778540, "relation_to_type": "type", "validated": true, "ani": 81.952, "matched_fragments": 923, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya dianthicola", "strain": "strain=NCPPB 453", "accession": "GCA_000365305.1", "taxid": 204039, "species_taxid": 204039, "relation_to_type": "type", "validated": true, "ani": 81.9414, "matched_fragments": 900, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya poaceiphila", "strain": "strain=NCPPB 569", "accession": "GCA_000406125.1", "taxid": 568768, "species_taxid": 568768, "relation_to_type": "type", "validated": true, "ani": 81.8402, "matched_fragments": 866, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya solani", "strain": "strain=IPO 2222", "accession": "GCA_001644705.1", "taxid": 1089444, "species_taxid": 1089444, "relation_to_type": "type", "validated": true, "ani": 81.8157, "matched_fragments": 907, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya solani", "strain": "strain=IPO 2222", "accession": "GCA_000400795.1", "taxid": 1089444, "species_taxid": 1089444, "relation_to_type": "type", "validated": true, "ani": 81.7144, "matched_fragments": 884, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya dadantii", "strain": "strain=NCPPB 898", "accession": "GCA_000406145.1", "taxid": 204038, "species_taxid": 204038, "relation_to_type": "type", "validated": true, "ani": 81.6514, "matched_fragments": 920, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dickeya undicola", "strain": "strain=2B12", "accession": "GCA_000784735.1", "taxid": 1577887, "species_taxid": 1577887, "relation_to_type": "type", "validated": true, "ani": 81.5271, "matched_fragments": 878, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Musicola keenii", "strain": "strain=A3967", "accession": "GCA_022761095.1", "taxid": 2884250, "species_taxid": 2884250, "relation_to_type": "type", "validated": true, "ani": 79.8704, "matched_fragments": 632, "total_fragments": 1455, "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": 79.4444, "matched_fragments": 454, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium polaris", "strain": "strain=NIBIO1006", "accession": "GCA_002307355.1", "taxid": 2042057, "species_taxid": 2042057, "relation_to_type": "type", "validated": true, "ani": 79.2952, "matched_fragments": 473, "total_fragments": 1455, "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": 78.9732, "matched_fragments": 477, "total_fragments": 1455, "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": 78.9662, "matched_fragments": 466, "total_fragments": 1455, "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": 78.9469, "matched_fragments": 343, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella pneumoniae", "strain": "strain=PartO-Kpneumoniae-RM8376", "accession": "GCA_022869665.1", "taxid": 573, "species_taxid": 573, "relation_to_type": "type", "validated": true, "ani": 78.8281, "matched_fragments": 295, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudocitrobacter corydidari", "strain": "", "accession": "GCA_021172065.1", "taxid": 2891570, "species_taxid": 2891570, "relation_to_type": "type", "validated": true, "ani": 78.6576, "matched_fragments": 307, "total_fragments": 1455, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003934295.1", "gtdb_species": "s__Dickeya lacustris", "ani": 99.9635, "matched_fragments": 1394, "total_fragments": 1455, "gtdb_taxonomy": 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_007858975.2", "gtdb_species": "s__Dickeya poaceiphila", "ani": 82.0216, "matched_fragments": 845, "total_fragments": 1455, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000406165.1", "gtdb_species": "s__Dickeya zeae", "ani": 81.9938, "matched_fragments": 917, "total_fragments": 1455, "gtdb_taxonomy": 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