{ "type": "genome", "identifier": "GCF_019048805.1", "organism": "Citrobacter braakii", "title": "Citrobacter braakii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019048805.1", "bioproject": "PRJNA224116", "biosample": "SAMN16357563", "wgs_master": "na", "refseq_category": "na", "taxid": "57706", "species_taxid": "57706", "organism_name": "Citrobacter braakii", "infraspecific_name": "strain=FDAARGOS 1421", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/06/28", "asm_name": "ASM1904880v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_019048805.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/048/805/GCF_019048805.1_ASM1904880v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5579607", "genome_size_ungapped": "5579607", "gc_percent": "52.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019048805.1-RS_2024_07_21", "annotation_date": "2024-07-21", "total_gene_count": "5440", "protein_coding_gene_count": "5191", "non_coding_gene_count": "126", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-06-28", "dateModified": "2021-06-28", "datePublished": "2021-06-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Citrobacter braakii" ], "sample_taxid": [ "57706" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Braunschweig" ], "sample_host_location_id": [], "data_size": "1.585 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)": "5579607", "Number of Sequences": "2", "Longest Sequences (bp)": "5561066", "N50 (bp)": "5561066", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.9", "Number of CDSs": "5303", "Average Protein Length": "307.1", "Coding Ratio (%)": "87.6", "Number of rRNAs": "25", "Number of tRNAs": "92", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Citrobacter braakii", "strain": "strain=FDAARGOS 1421", "accession": "GCA_019048805.1", "taxid": 57706, "species_taxid": 57706, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1859, "total_fragments": 1859, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Citrobacter braakii", "strain": "strain=ATCC 51113", "accession": "GCA_002075345.1", "taxid": 57706, "species_taxid": 57706, "relation_to_type": "type", "validated": true, "ani": 99.965, "matched_fragments": 1791, "total_fragments": 1859, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Citrobacter europaeus", "strain": "strain=97/79", "accession": "GCA_900079995.3", "taxid": 1914243, "species_taxid": 1914243, "relation_to_type": "type", "validated": true, "ani": 93.3243, "matched_fragments": 1392, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter arsenatis", "strain": "strain=LY-1", "accession": "GCA_004353845.1", "taxid": 2546350, "species_taxid": 2546350, "relation_to_type": "type", "validated": true, "ani": 93.0619, "matched_fragments": 1423, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter portucalensis", "strain": "strain=A60", "accession": "GCA_002042885.1", "taxid": 1639133, "species_taxid": 1639133, "relation_to_type": "type", "validated": true, "ani": 92.5105, "matched_fragments": 1346, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter freundii", "strain": "strain=ATCC 8090", "accession": "GCA_011064845.1", "taxid": 546, "species_taxid": 546, "relation_to_type": "type", "validated": true, "ani": 92.4207, "matched_fragments": 1381, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter freundii", "strain": "strain=NBRC 12681", "accession": "GCA_000759735.1", "taxid": 546, "species_taxid": 546, "relation_to_type": "type", "validated": true, "ani": 92.3656, "matched_fragments": 1345, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter pasteurii", "strain": "strain=FDAARGOS 1424", "accession": "GCA_019047765.1", "taxid": 1563222, "species_taxid": 1563222, "relation_to_type": "type", "validated": true, "ani": 90.0512, "matched_fragments": 1301, "total_fragments": 1859, "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": 83.0682, "matched_fragments": 1003, "total_fragments": 1859, "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": 83.0138, "matched_fragments": 1061, "total_fragments": 1859, "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": 81.6899, "matched_fragments": 868, "total_fragments": 1859, "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": 81.6256, "matched_fragments": 890, "total_fragments": 1859, "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": 81.3624, "matched_fragments": 872, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aeromonas jandaei", "strain": "strain=FDAARGOS_1523", "accession": "GCA_020341535.1", 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"validated": true, "ani": 76.7288, "matched_fragments": 100, "total_fragments": 1859, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002075345.1", "gtdb_species": "s__Citrobacter braakii", "ani": 99.965, "matched_fragments": 1791, "total_fragments": 1859, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "96.30", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.77", "num_clustered_genomes": 154, "status": "conclusive" }, { "accession": "GCF_900079995.3", "gtdb_species": "s__Citrobacter europaeus", "ani": 93.3279, "matched_fragments": 1391, "total_fragments": 1859, "gtdb_taxonomy": 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