{ "type": "genome", "identifier": "GCF_018987305.1", "organism": "Leclercia pneumoniae", "title": "Leclercia pneumoniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University Hospital Leipzig", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018987305.1", "bioproject": "PRJNA224116", "biosample": "SAMN19717142", "wgs_master": "na", "refseq_category": "na", "taxid": "2815358", "species_taxid": "2815358", "organism_name": "Leclercia pneumoniae", "infraspecific_name": "strain=49125", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/06/23", "asm_name": "ASM1898730v1", "asm_submitter": "University Hospital Leipzig", "gbrs_paired_asm": "GCA_018987305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/987/305/GCF_018987305.1_ASM1898730v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4392327", "genome_size_ungapped": "4392327", "gc_percent": "55.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018987305.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "4272", "protein_coding_gene_count": "4050", "non_coding_gene_count": "122", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-06-23", "dateModified": "2021-06-23", "datePublished": "2021-06-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Leclercia pneumoniae" ], "sample_taxid": [ "2815358" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "pneumonia" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Leipzig" ], "sample_host_location_id": [], "data_size": "1.246 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)": "4392327", "Number of Sequences": "1", "Longest Sequences (bp)": "4392327", "N50 (bp)": "4392327", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.0", "Number of CDSs": "4191", "Average Protein Length": "309.3", "Coding Ratio (%)": "88.5", "Number of rRNAs": "22", "Number of tRNAs": "87", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leclercia pneumoniae", "strain": "strain=49125", "accession": "GCA_018987305.1", "taxid": 2815358, "species_taxid": 2815358, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1464, "total_fragments": 1464, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leclercia pneumoniae", "strain": "strain=49125", "accession": "GCA_017348915.1", "taxid": 2815358, "species_taxid": 2815358, "relation_to_type": "type", "validated": true, "ani": 99.9961, "matched_fragments": 1461, "total_fragments": 1464, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterobacter cancerogenus", "strain": "strain=FDAARGOS 1428", "accession": "GCA_019047785.1", "taxid": 69218, "species_taxid": 69218, "relation_to_type": "type", "validated": true, "ani": 84.6943, "matched_fragments": 1072, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter cancerogenus", "strain": "", "accession": "GCA_900185905.1", "taxid": 69218, "species_taxid": 69218, "relation_to_type": "type", "validated": true, "ani": 84.5166, "matched_fragments": 1051, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia adecarboxylata", "strain": "strain=FDAARGOS_1505", "accession": "GCA_020097395.1", "taxid": 83655, "species_taxid": 83655, "relation_to_type": "suspected-type", "validated": true, "ani": 84.4316, "matched_fragments": 1138, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. hormaechei", "strain": "strain=ATCC 49162", "accession": "GCA_001875655.1", "taxid": 301105, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 84.3293, "matched_fragments": 1052, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter oligotrophicus", "strain": "strain=CCA6", "accession": "GCA_009176645.1", "taxid": 2478464, "species_taxid": 2478464, "relation_to_type": "type", "validated": true, "ani": 84.3072, "matched_fragments": 1067, "total_fragments": 1464, "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": 84.3057, "matched_fragments": 1069, "total_fragments": 1464, "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": 84.2913, "matched_fragments": 1059, "total_fragments": 1464, "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": 84.2436, "matched_fragments": 1020, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. hoffmannii", "strain": "strain=DSM 14563", "accession": "GCA_001729745.1", "taxid": 1812934, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 84.2231, "matched_fragments": 1050, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia adecarboxylata", "strain": "strain=ATCC 23216", "accession": "GCA_000735515.1", "taxid": 83655, "species_taxid": 83655, "relation_to_type": "suspected-type", "validated": true, "ani": 84.2177, "matched_fragments": 1107, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia adecarboxylata", "strain": "strain=NBRC 102595", "accession": "GCA_001515505.1", "taxid": 83655, "species_taxid": 83655, "relation_to_type": "suspected-type", "validated": true, "ani": 84.1994, "matched_fragments": 1127, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. hormaechei", "strain": "strain=ATCC 49162", "accession": "GCA_000213995.1", "taxid": 301105, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 84.1969, "matched_fragments": 1047, "total_fragments": 1464, "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": 84.186, "matched_fragments": 1081, "total_fragments": 1464, "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": 84.0024, "matched_fragments": 1057, "total_fragments": 1464, "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": 83.9443, "matched_fragments": 1035, "total_fragments": 1464, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017348915.1", "gtdb_species": "s__UBA7405 sp000755535", "ani": 99.9955, "matched_fragments": 1462, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "97.85", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 10, "status": "conclusive" }, { "accession": "GCA_002469605.1", "gtdb_species": "s__UBA7405 sp002469605", "ani": 85.3881, "matched_fragments": 796, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405", "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_019047785.1", "gtdb_species": "s__Enterobacter cancerogenus", "ani": 84.6984, "matched_fragments": 1071, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_006874705.1", "gtdb_species": "s__Leclercia adecarboxylata_C", "ani": 84.6676, "matched_fragments": 1138, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_006171285.1", "gtdb_species": "s__Leclercia adecarboxylata_A", "ani": 84.6391, "matched_fragments": 1165, "total_fragments": 1464, "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": "GCA_002360945.1", "gtdb_species": "s__Leclercia adecarboxylata_B", "ani": 84.4426, "matched_fragments": 1114, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009176645.1", "gtdb_species": "s__Enterobacter oligotrophicus", "ani": 84.3205, "matched_fragments": 1065, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.55", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003594935.1", "gtdb_species": "s__Enterobacter huaxiensis", "ani": 84.3041, "matched_fragments": 1070, "total_fragments": 1464, "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_900324475.1", "gtdb_species": "s__Enterobacter bugandensis", "ani": 84.3032, "matched_fragments": 1067, "total_fragments": 1464, "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": "GCA_901472455.1", "gtdb_species": "s__Leclercia adecarboxylata", "ani": 84.2671, "matched_fragments": 1121, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 86, "status": "-" }, { "accession": "GCF_011754535.1", "gtdb_species": "s__Enterobacter cloacae_N", "ani": 84.2335, "matched_fragments": 1062, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003594915.1", "gtdb_species": "s__Enterobacter chuandaensis", "ani": 84.2331, "matched_fragments": 1029, "total_fragments": 1464, "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_001729745.1", "gtdb_species": "s__Enterobacter hormaechei_A", "ani": 84.2143, "matched_fragments": 1052, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.63", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 1867, "status": "-" }, { "accession": "GCF_008364625.1", "gtdb_species": "s__Enterobacter dykesii", "ani": 84.2012, "matched_fragments": 1020, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.5795, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_009755685.1", "gtdb_species": "s__Enterobacter sp000568095", "ani": 84.1975, "matched_fragments": 1065, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0476, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "98.04", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_004331265.1", "gtdb_species": "s__Enterobacter wuhouensis", "ani": 84.1948, "matched_fragments": 1080, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "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_007035645.1", "gtdb_species": "s__Enterobacter asburiae_B", "ani": 84.1831, "matched_fragments": 1076, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.8818, "mean_intra_species_ani": "98.31", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 70, "status": "-" }, { "accession": "GCF_000025565.1", "gtdb_species": "s__Enterobacter cloacae", "ani": 84.1791, "matched_fragments": 1074, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.05", "min_intra_species_ani": "95.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.80", "num_clustered_genomes": 129, "status": "-" }, { "accession": "GCF_000211415.1", "gtdb_species": "s__Enterobacter mori", "ani": 84.1023, "matched_fragments": 1043, "total_fragments": 1464, "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_003057745.1", "gtdb_species": "s__Enterobacter sp003057745", "ani": 83.8611, "matched_fragments": 994, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "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_009363175.1", "gtdb_species": "s__Citrobacter_A telavivensis", "ani": 81.7646, "matched_fragments": 841, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004353845.1", "gtdb_species": "s__Citrobacter freundii_E", "ani": 81.4066, "matched_fragments": 801, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010231475.1", "gtdb_species": "s__Citrobacter sp010231475", "ani": 81.0343, "matched_fragments": 752, "total_fragments": 1464, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 30.5, "optimum_tmp": 38.5, "optimum_ph": null, "genome_size": 4940780.75, "gc_content": 55.7, "coding_genes": 4321.5, "rRNA16S_genes": 8.0, "tRNA_genes": 84.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Leclercia", "pneumoniae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }