{ "type": "genome", "identifier": "GCF_000321045.1", "organism": "Phytobacter massiliensis JC163", "title": "Phytobacter massiliensis JC163", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Laboratoire URMITE CNRS 6236", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000321045.1", "bioproject": "PRJNA224116", "biosample": "SAMEA2272705", "wgs_master": "CAEO00000000.1", "refseq_category": "reference genome", "taxid": "1095768", "species_taxid": "1485952", "organism_name": "Phytobacter massiliensis JC163", "infraspecific_name": "strain=type strain: JC163", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/12/06", "asm_name": "ASM32104v2", "asm_submitter": "Laboratoire URMITE CNRS 6236", "gbrs_paired_asm": "GCA_000321045.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/321/045/GCF_000321045.1_ASM32104v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5003540", "genome_size_ungapped": "4922247", "gc_percent": "55.500000", "replicon_count": "0", "scaffold_count": "77", "contig_count": "236", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000321045.1-RS_2024_06_10", "annotation_date": "2024-06-10", "total_gene_count": "4823", "protein_coding_gene_count": "4514", "non_coding_gene_count": "95", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-12-06", "dateModified": "2012-12-06", "datePublished": "2012-12-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Phytobacter massiliensis JC163" ], "sample_taxid": [ "1095768" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Senegal" ], "sample_host_location_id": [], "data_size": "1.396 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.44, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5001662", "Number of Sequences": "65", "Longest Sequences (bp)": "2115321", "N50 (bp)": "785945", "Gap Ratio (%)": "1.625420", "GCcontent (%)": "55.5", "Number of CDSs": "4604", "Average Protein Length": "307.0", "Coding Ratio (%)": "84.8", "Number of rRNAs": "3", "Number of tRNAs": "72", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 81.8677, "matched_fragments": 862, "total_fragments": 1651, "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": 81.7868, "matched_fragments": 869, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella quasipneumoniae subsp. quasipneumoniae", "strain": "strain=01A030", "accession": "GCA_000751755.1", "taxid": 1667327, "species_taxid": 1463165, "relation_to_type": "type", "validated": true, "ani": 81.7777, "matched_fragments": 831, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, 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"matched_fragments": 842, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella quasipneumoniae", "strain": "strain=FDAARGOS_1503", "accession": "GCA_020099175.1", "taxid": 1463165, "species_taxid": 1463165, "relation_to_type": "type", "validated": true, "ani": 81.6703, "matched_fragments": 844, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. xiangfangensis", "strain": "strain=LMG27195", "accession": "GCA_001729785.1", "taxid": 1296536, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 81.5281, "matched_fragments": 884, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudescherichia vulneris", "strain": "strain=NCTC12130", "accession": "GCA_900450975.1", "taxid": 566, "species_taxid": 566, "relation_to_type": "type", "validated": true, "ani": 81.52, "matched_fragments": 895, 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"status": "below_threshold" }, { "organism_name": "Klebsiella variicola", "strain": "strain=DSM 15968", "accession": "GCA_000828055.2", "taxid": 244366, "species_taxid": 244366, "relation_to_type": "type", "validated": true, "ani": 81.3108, "matched_fragments": 864, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter amalonaticus", "strain": "strain=JCM 1661", "accession": "GCA_018323885.1", "taxid": 35703, "species_taxid": 35703, "relation_to_type": "type", "validated": true, "ani": 81.2648, "matched_fragments": 791, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter universalis", "strain": "strain=NCTC 9529", "accession": "GCA_000409325.1", "taxid": 535744, "species_taxid": 535744, "relation_to_type": "type", "validated": true, "ani": 81.2039, "matched_fragments": 832, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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562, "relation_to_type": "neotype", "validated": true, "ani": 80.687, "matched_fragments": 705, "total_fragments": 1651, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.44, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000321045.1", "gtdb_species": "s__Phytobacter massiliensis", "ani": 99.9999, "matched_fragments": 1643, "total_fragments": 1651, "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": "conclusive" }, { "accession": "GCA_004346725.1", "gtdb_species": "s__Phytobacter diazotrophicus", "ani": 82.7655, "matched_fragments": 1072, "total_fragments": 1651, "gtdb_taxonomy": 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