{ "type": "genome", "identifier": "GCF_004115925.1", "organism": "Lelliottia nimipressuralis", "title": "Lelliottia nimipressuralis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Gothenburg - CCUG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004115925.1", "bioproject": "PRJNA224116", "biosample": "SAMN10768966", "wgs_master": "SDDX00000000.1", "refseq_category": "na", "taxid": "69220", "species_taxid": "69220", "organism_name": "Lelliottia nimipressuralis", "infraspecific_name": "strain=CCUG 25894", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/28", "asm_name": "ASM411592v1", "asm_submitter": "University of Gothenburg - CCUG", "gbrs_paired_asm": "GCA_004115925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/115/925/GCF_004115925.1_ASM411592v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4616251", "genome_size_ungapped": "4616251", "gc_percent": "55.000000", "replicon_count": "0", "scaffold_count": "67", "contig_count": "67", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004115925.1-RS_2024_06_24", "annotation_date": "2024-06-24", "total_gene_count": "4431", "protein_coding_gene_count": "4256", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-28", "dateModified": "2019-01-28", "datePublished": "2019-01-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Lelliottia nimipressuralis" ], "sample_taxid": [ "69220" ], "sample_host_organism": [ "Elm tree" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.312 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4616251", "Number of Sequences": "67", "Longest Sequences (bp)": "509082", "N50 (bp)": "236780", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.8", "Number of CDSs": "4291", "Average Protein Length": "317.8", "Coding Ratio (%)": "88.6", "Number of rRNAs": "3", "Number of tRNAs": "64", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lelliottia nimipressuralis", "strain": "strain=CCUG 25894", "accession": "GCA_004115925.1", "taxid": 69220, "species_taxid": 69220, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1506, "total_fragments": 1507, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lelliottia aquatilis", "strain": "strain=6331-17", "accession": "GCA_002923025.1", "taxid": 2080838, "species_taxid": 2080838, "relation_to_type": "type", "validated": true, "ani": 89.997, "matched_fragments": 1280, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lelliottia amnigena", "strain": "strain=NBRC 105700", "accession": "GCA_001514515.1", "taxid": 61646, "species_taxid": 61646, "relation_to_type": "type", "validated": true, "ani": 85.7742, "matched_fragments": 1163, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lelliottia amnigena", "strain": "strain=FDAARGOS 1444", "accession": "GCA_019047465.1", "taxid": 61646, "species_taxid": 61646, "relation_to_type": "type", "validated": true, "ani": 85.7557, "matched_fragments": 1168, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lelliottia amnigena", "strain": "strain=LMG 2784", "accession": "GCA_002553545.1", "taxid": 61646, "species_taxid": 61646, "relation_to_type": "type", "validated": true, "ani": 85.7205, "matched_fragments": 1141, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter asburiae", "strain": "strain=FDAARGOS_892", "accession": "GCA_016027695.1", "taxid": 61645, "species_taxid": 61645, "relation_to_type": "type", "validated": true, "ani": 85.2, "matched_fragments": 1073, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter asburiae", "strain": "strain=ATCC 35953", "accession": "GCA_001521715.1", "taxid": 61645, "species_taxid": 61645, "relation_to_type": "type", "validated": true, "ani": 85.168, "matched_fragments": 1083, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 85.0773, "matched_fragments": 1153, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=FDAARGOS 1430", "accession": "GCA_019047025.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 84.9275, "matched_fragments": 1146, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter bugandensis", "strain": "", "accession": "GCA_900324475.1", "taxid": 881260, "species_taxid": 881260, "relation_to_type": "type", "validated": true, "ani": 84.8725, "matched_fragments": 1106, "total_fragments": 1507, "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": 84.8662, "matched_fragments": 1086, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter vonholyi", "strain": "strain=E13", "accession": "GCA_008364555.1", "taxid": 2797505, "species_taxid": 2797505, "relation_to_type": "type", "validated": true, "ani": 84.8461, "matched_fragments": 1089, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. oharae", "strain": "strain=FDAARGOS_1533", "accession": "GCA_020097195.1", "taxid": 301102, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 84.8099, "matched_fragments": 1107, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter bugandensis", "strain": "strain=FDAARGOS 1427", "accession": "GCA_019046905.1", "taxid": 881260, "species_taxid": 881260, "relation_to_type": "type", "validated": true, "ani": 84.7889, "matched_fragments": 1133, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter cloacae", "strain": "strain=DSM 30054", "accession": "GCA_021469225.1", "taxid": 550, "species_taxid": 550, "relation_to_type": "type", "validated": true, "ani": 84.7596, "matched_fragments": 1099, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. oharae", "strain": "strain=DSM 16687", "accession": "GCA_001729705.1", "taxid": 301102, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 84.7092, "matched_fragments": 1103, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei", "strain": "strain=FDAARGOS 1433", "accession": "GCA_019048245.1", "taxid": 158836, "species_taxid": 158836, "relation_to_type": "suspected-type", "validated": true, "ani": 84.708, "matched_fragments": 1087, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 84.6772, "matched_fragments": 1093, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter ludwigii", "strain": "strain=EN-119", "accession": "GCA_001750725.1", "taxid": 299767, "species_taxid": 299767, "relation_to_type": "type", "validated": true, "ani": 84.5255, "matched_fragments": 1119, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter ludwigii", "strain": "strain=EN-119", "accession": "GCA_000818595.1", "taxid": 299767, "species_taxid": 299767, "relation_to_type": "type", "validated": true, "ani": 84.5134, "matched_fragments": 1121, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter ludwigii", "strain": "strain=FDAARGOS 1436", "accession": "GCA_019047005.1", "taxid": 299767, "species_taxid": 299767, "relation_to_type": "type", "validated": true, "ani": 84.4721, "matched_fragments": 1110, "total_fragments": 1507, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004115925.1", "gtdb_species": "s__Lelliottia nimipressuralis", "ani": 100.0, "matched_fragments": 1506, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.29", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCA_002271215.1", "gtdb_species": "s__Lelliottia jeotgali", "ani": 90.02, "matched_fragments": 1272, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_009668015.1", "gtdb_species": "s__Lelliottia sp009668015", "ani": 87.7845, "matched_fragments": 1176, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia", "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_000016325.1", "gtdb_species": "s__Lelliottia sp000016325", "ani": 85.8945, "matched_fragments": 1171, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.60", "min_intra_species_ani": "95.60", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900635465.1", "gtdb_species": "s__Lelliottia amnigena", "ani": 85.7418, "matched_fragments": 1162, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "98.20", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_003634515.1", "gtdb_species": "s__Enterobacter asburiae_A", "ani": 85.06, "matched_fragments": 1127, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.0274, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003594935.1", "gtdb_species": "s__Enterobacter huaxiensis", "ani": 84.951, "matched_fragments": 1150, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.98", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003594915.1", "gtdb_species": "s__Enterobacter chuandaensis", "ani": 84.9469, "matched_fragments": 1108, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008080435.1", "gtdb_species": "s__Enterobacter asburiae_C", "ani": 84.9415, "matched_fragments": 1103, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.5575, "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_900324475.1", "gtdb_species": "s__Enterobacter bugandensis", "ani": 84.8819, "matched_fragments": 1105, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 115, "status": "-" }, { "accession": "GCF_000211415.1", "gtdb_species": "s__Enterobacter mori", "ani": 84.8769, "matched_fragments": 1103, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "96.13", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_013375935.1", "gtdb_species": "s__Enterobacter cloacae_O", "ani": 84.539, "matched_fragments": 1125, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.68", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_011290365.1", "gtdb_species": "s__Leclercia sp003024485", "ani": 84.4351, "matched_fragments": 1071, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.06", "min_intra_species_ani": "98.06", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006171285.1", "gtdb_species": "s__Leclercia adecarboxylata_A", "ani": 84.4202, "matched_fragments": 1110, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002902985.1", "gtdb_species": "s__Leclercia sp002902985", "ani": 83.9617, "matched_fragments": 1059, "total_fragments": 1507, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "96.37", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 16, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": null, "genome_size": 4826850.0, "gc_content": 55.7, "coding_genes": 4425.0, "rRNA16S_genes": 7.0, "tRNA_genes": 83.0, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Lelliottia", "nimipressuralis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }