{ "type": "genome", "identifier": "GCF_002843235.3", "organism": "Providencia huaxiensis", "title": "Providencia huaxiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "West China Hospital, Sichuan University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002843235.3", "bioproject": "PRJNA224116", "biosample": "SAMN07508212", "wgs_master": "na", "refseq_category": "na", "taxid": "2027290", "species_taxid": "2027290", "organism_name": "Providencia huaxiensis", "infraspecific_name": "strain=WCHPr000369", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/08/22", "asm_name": "ASM284323v3", "asm_submitter": "West China Hospital, Sichuan University", "gbrs_paired_asm": "GCA_002843235.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/843/235/GCF_002843235.3_ASM284323v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4800413", "genome_size_ungapped": "4800413", "gc_percent": "41.500000", "replicon_count": "6", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002843235.3-RS_2024_09_23", "annotation_date": "2024-09-23", "total_gene_count": "4542", "protein_coding_gene_count": "4352", "non_coding_gene_count": "103", "pubmed_id": "32176782;31162027" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-08-22", "dateModified": "2019-08-22", "datePublished": "2019-08-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Providencia huaxiensis" ], "sample_taxid": [ "2027290" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Sichuan, Chengdu" ], "sample_host_location_id": [], "data_size": "1.361 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)": "4800413", "Number of Sequences": "6", "Longest Sequences (bp)": "4573616", "N50 (bp)": "4573616", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "41.3", "Number of CDSs": "4457", "Average Protein Length": "306.5", "Coding Ratio (%)": "85.4", "Number of rRNAs": "22", "Number of tRNAs": "77", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Providencia huaxiensis", "strain": "strain=WCHPr000369", "accession": "GCA_002843235.3", "taxid": 2027290, "species_taxid": 2027290, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1593, "total_fragments": 1596, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Providencia rettgeri", "strain": "strain=FDAARGOS 1450", "accession": "GCA_019048105.1", "taxid": 587, "species_taxid": 587, "relation_to_type": "suspected-type", "validated": true, "ani": 91.4633, "matched_fragments": 1230, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia vermicola", "strain": "strain=DSM 17385", "accession": "GCA_020381325.1", "taxid": 333965, "species_taxid": 333965, "relation_to_type": "suspected-type", "validated": true, "ani": 83.07, "matched_fragments": 1017, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia heimbachae", "strain": "strain=NCTC12003", "accession": "GCA_900475855.1", "taxid": 333962, "species_taxid": 333962, "relation_to_type": "type", "validated": true, "ani": 81.3768, "matched_fragments": 864, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia heimbachae", "strain": "strain=ATCC 35613", "accession": "GCA_001655055.1", "taxid": 333962, "species_taxid": 333962, "relation_to_type": "type", "validated": true, "ani": 81.1269, "matched_fragments": 857, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia rustigianii", "strain": "strain=NCTC11802", "accession": "GCA_900455075.1", "taxid": 158850, "species_taxid": 158850, "relation_to_type": "type", "validated": true, "ani": 81.0048, "matched_fragments": 717, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia alcalifaciens", "strain": "strain=DSM 30120", "accession": "GCA_000173415.1", "taxid": 126385, "species_taxid": 126385, "relation_to_type": "type", "validated": true, "ani": 80.9504, "matched_fragments": 675, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia rustigianii", "strain": "strain=DSM 4541", "accession": "GCA_000156395.1", "taxid": 158850, "species_taxid": 158850, "relation_to_type": "type", "validated": true, "ani": 80.8184, "matched_fragments": 710, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia manganoxydans", "strain": "strain=LLDRA6", "accession": "GCA_016618195.1", "taxid": 2923283, "species_taxid": 2923283, "relation_to_type": "type", "validated": true, "ani": 80.4682, "matched_fragments": 646, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia burhodogranariea", "strain": "strain=DSM 19968", "accession": "GCA_000314855.2", "taxid": 516074, "species_taxid": 516074, "relation_to_type": "type", "validated": true, "ani": 79.8991, "matched_fragments": 622, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hafnia paralvei", "strain": "strain=ATCC 29927", "accession": "GCA_023698525.1", "taxid": 546367, "species_taxid": 546367, "relation_to_type": "type", "validated": true, "ani": 79.6712, "matched_fragments": 140, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium colocasium", "strain": "strain=LJ1", "accession": "GCA_020181655.1", "taxid": 2878098, "species_taxid": 2878098, "relation_to_type": "type", "validated": true, "ani": 79.0365, "matched_fragments": 111, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenophonus apicola", "strain": "strain=ArsBeeUS", "accession": "GCA_020268605.1", "taxid": 2879119, "species_taxid": 2879119, "relation_to_type": "type", "validated": true, "ani": 78.2973, "matched_fragments": 156, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus bovienii", "strain": "strain=T228", "accession": "GCA_024721015.1", "taxid": 40576, "species_taxid": 40576, "relation_to_type": "type", "validated": true, "ani": 77.9376, "matched_fragments": 173, "total_fragments": 1596, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002843235.3", "gtdb_species": "s__Providencia huaxiensis", "ani": 100.0, "matched_fragments": 1593, "total_fragments": 1596, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.69", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCF_003936755.2", "gtdb_species": "s__Providencia rettgeri_E", "ani": 94.1219, "matched_fragments": 1274, 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Providencia", "huaxiensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }