{ "type": "genome", "identifier": "GCA_948435835.1", "organism": "Citrobacter amalonaticus", "title": "Citrobacter amalonaticus", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "EMG", "publication": [ {} ], "properties": { "assembly_accession": "GCA_948435835.1", "bioproject": "PRJEB57940", "biosample": "SAMEA112247615", "wgs_master": "CAOJHD000000000.1", "refseq_category": "na", "taxid": "35703", "species_taxid": "35703", "organism_name": "Citrobacter amalonaticus", "infraspecific_name": "", "isolate": "SRR17794281_bin.11_metawrap_v1.3_MAG", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/02/03", "asm_name": "SRR17794281_bin.11_metawrap_v1.3_MAG", "submitter": "EMG", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/948/435/835/GCA_948435835.1_SRR17794281_bin.11_metawrap_v1.3_MAG", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-02-03", "dateModified": "2023-02-03", "datePublished": "2023-02-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Citrobacter amalonaticus" ], "sample_taxid": [ "35703" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.357 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4762996", "Number of Sequences": "25", "Longest Sequences (bp)": "659944", "N50 (bp)": "425481", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.4", "Number of CDSs": "4395", "Average Protein Length": "320.2", "Coding Ratio (%)": "88.6", "Number of rRNAs": "2", "Number of tRNAs": "66", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Citrobacter amalonaticus", "strain": "strain=FDAARGOS_1489", "accession": "GCA_020099335.1", "taxid": 35703, "species_taxid": 35703, "relation_to_type": "type", "validated": true, "ani": 99.5456, "matched_fragments": 1518, "total_fragments": 1573, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Citrobacter amalonaticus", "strain": "strain=JCM 1661", "accession": "GCA_018323885.1", "taxid": 35703, "species_taxid": 35703, "relation_to_type": "type", "validated": true, "ani": 99.5235, "matched_fragments": 1518, "total_fragments": 1573, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Citrobacter farmeri", "strain": "strain=FDAARGOS 1423", "accession": "GCA_019048065.1", "taxid": 67824, "species_taxid": 67824, "relation_to_type": "type", "validated": true, "ani": 91.4527, "matched_fragments": 1390, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_015965555.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 84.8419, "matched_fragments": 1118, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_021278985.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 84.7805, "matched_fragments": 1164, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. enterica", "strain": "strain=PartC-Senterica-RM8376", "accession": "GCA_022869965.1", "taxid": 59201, "species_taxid": 28901, "relation_to_type": "suspected-type", "validated": true, "ani": 82.7706, "matched_fragments": 965, "total_fragments": 1573, "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": 82.058, "matched_fragments": 855, "total_fragments": 1573, "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": 81.7438, "matched_fragments": 886, "total_fragments": 1573, "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": 81.7198, "matched_fragments": 886, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella oxytoca", "strain": "strain=NBRC 105695", "accession": "GCA_001598695.1", "taxid": 571, "species_taxid": 571, "relation_to_type": "type", "validated": true, "ani": 81.1175, "matched_fragments": 853, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella oxytoca", "strain": "strain=DSM 5175", "accession": "GCA_020115535.1", "taxid": 571, "species_taxid": 571, "relation_to_type": "type", "validated": true, "ani": 81.0524, "matched_fragments": 866, "total_fragments": 1573, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018323885.1", "gtdb_species": "s__Citrobacter_A amalonaticus", "ani": 99.5235, "matched_fragments": 1518, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 59, "status": "conclusive" }, { "accession": "GCF_018252635.1", "gtdb_species": "s__Citrobacter_A amalonaticus_E", "ani": 92.6768, "matched_fragments": 1376, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000981805.1", "gtdb_species": "s__Citrobacter_A amalonaticus_C", "ani": 91.9542, "matched_fragments": 1377, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "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": 91.8567, "matched_fragments": 1398, "total_fragments": 1573, "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_019048065.1", "gtdb_species": "s__Citrobacter_A farmeri", "ani": 91.4527, "matched_fragments": 1390, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_000759815.1", "gtdb_species": "s__Citrobacter_A rodentium", "ani": 84.8451, "matched_fragments": 1124, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000321045.1", "gtdb_species": "s__Phytobacter massiliensis", "ani": 81.1557, "matched_fragments": 789, "total_fragments": 1573, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Phytobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 34.5, "optimum_tmp": 28.0, "optimum_ph": null, "genome_size": 5136887.889, "gc_content": 53.338, "coding_genes": 4864.5, "rRNA16S_genes": 7.0, "tRNA_genes": 86.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.857, "range_salinity": 0.5, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Enterobacteriaceae", "g__Citrobacter_A", "s__Citrobacter_A amalonaticus" ], "_genome_taxon": [ "Citrobacter", "amalonaticus", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Enterobacterales", "f__Enterobacteriaceae", "g__Citrobacter_A", "s__Citrobacter_A amalonaticus", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Enterobacterales", "Enterobacteriaceae", "Citrobacter", "A", "Citrobacter", "A", "amalonaticus" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }