{ "type": "genome", "identifier": "GCF_003818115.1", "organism": "Citrobacter youngae", "title": "Citrobacter youngae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Gothenburg - CCUG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003818115.1", "bioproject": "PRJNA224116", "biosample": "SAMN10440282", "wgs_master": "RPOI00000000.1", "refseq_category": "na", "taxid": "133448", "species_taxid": "133448", "organism_name": "Citrobacter youngae", "infraspecific_name": "strain=CCUG 30791", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/11/25", "asm_name": "ASM381811v1", "asm_submitter": "University of Gothenburg - CCUG", "gbrs_paired_asm": "GCA_003818115.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/818/115/GCF_003818115.1_ASM381811v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4819610", "genome_size_ungapped": "4819610", "gc_percent": "52.000000", "replicon_count": "0", "scaffold_count": "55", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003818115.1-RS_2024_03_30", "annotation_date": "2024-03-30", "total_gene_count": "4717", "protein_coding_gene_count": "4526", "non_coding_gene_count": "96", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-11-25", "dateModified": "2018-11-25", "datePublished": "2018-11-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Citrobacter youngae" ], "sample_taxid": [ "133448" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: South Carolina" ], "sample_host_location_id": [], "data_size": "1.375 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)": "4819610", "Number of Sequences": "55", "Longest Sequences (bp)": "479055", "N50 (bp)": "211550", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.8", "Number of CDSs": "4589", "Average Protein Length": "308.4", "Coding Ratio (%)": "88.1", "Number of rRNAs": "9", "Number of tRNAs": "72", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Citrobacter youngae", "strain": "strain=CCUG 30791", "accession": "GCA_003818115.1", "taxid": 133448, "species_taxid": 133448, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1576, "total_fragments": 1578, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Citrobacter youngae", "strain": "strain=NCTC13709", "accession": "GCA_900638065.1", "taxid": 133448, "species_taxid": 133448, "relation_to_type": "type", "validated": true, "ani": 99.9899, "matched_fragments": 1577, "total_fragments": 1578, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Citrobacter pasteurii", "strain": "strain=CIP 55.13", "accession": "GCA_000826205.1", "taxid": 1563222, "species_taxid": 1563222, "relation_to_type": "type", "validated": true, "ani": 95.4225, "matched_fragments": 1387, "total_fragments": 1578, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Citrobacter pasteurii", "strain": "strain=FDAARGOS 1424", "accession": "GCA_019047765.1", "taxid": 1563222, "species_taxid": 1563222, "relation_to_type": "type", "validated": true, "ani": 95.4133, "matched_fragments": 1399, "total_fragments": 1578, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": 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"GCA_002042885.1", "taxid": 1639133, "species_taxid": 1639133, "relation_to_type": "type", "validated": true, "ani": 90.5594, "matched_fragments": 1292, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter europaeus", "strain": "strain=97/79", "accession": "GCA_900079995.3", "taxid": 1914243, "species_taxid": 1914243, "relation_to_type": "type", "validated": true, "ani": 90.3895, "matched_fragments": 1334, "total_fragments": 1578, "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": 90.1698, "matched_fragments": 1324, "total_fragments": 1578, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_021278985.1", "taxid": 67825, "species_taxid": 67825, 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"min_intra_species_af": "0.87", "num_clustered_genomes": 45, "status": "conclusive" }, { "accession": "GCF_005281345.1", "gtdb_species": "s__Citrobacter sp005281345", "ani": 93.9943, "matched_fragments": 1390, "total_fragments": 1578, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.53", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011064845.1", "gtdb_species": "s__Citrobacter freundii", "ani": 91.702, "matched_fragments": 1346, "total_fragments": 1578, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.89", 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