{ "type": "genome", "identifier": "GCF_020381325.1", "organism": "Providencia vermicola", "title": "Providencia vermicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "UNIVERSITY OF NAPLES \"FEDERICO II\"", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020381325.1", "bioproject": "PRJNA224116", "biosample": "SAMN18809890", "wgs_master": "JAGSPI000000000.1", "refseq_category": "reference genome", "taxid": "333965", "species_taxid": "333965", "organism_name": "Providencia vermicola", "infraspecific_name": "strain=DSM 17385", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/10/08", "asm_name": "ASM2038132v1", "asm_submitter": "UNIVERSITY OF NAPLES \"FEDERICO II\"", "gbrs_paired_asm": "GCA_020381325.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/381/325/GCF_020381325.1_ASM2038132v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4237400", "genome_size_ungapped": "4237283", "gc_percent": "41.000000", "replicon_count": "1", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020381325.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3843", "protein_coding_gene_count": "3741", "non_coding_gene_count": "80", "pubmed_id": "34598677" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-10-08", "dateModified": "2021-10-08", "datePublished": "2021-10-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Providencia vermicola" ], "sample_taxid": [ "333965" ], "sample_host_organism": [ "Steinernema thermophilum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "1.204 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)": "4237400", "Number of Sequences": "19", "Longest Sequences (bp)": "548405", "N50 (bp)": "344020", "Gap Ratio (%)": "0.003257", "GCcontent (%)": "41.1", "Number of CDSs": "3766", "Average Protein Length": "321.9", "Coding Ratio (%)": "85.8", "Number of rRNAs": "2", "Number of tRNAs": "68", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, 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1402, "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": 81.2155, "matched_fragments": 816, "total_fragments": 1402, "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": 80.8669, "matched_fragments": 722, "total_fragments": 1402, "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": 80.822, "matched_fragments": 698, "total_fragments": 1402, "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": 80.8066, "matched_fragments": 735, "total_fragments": 1402, "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": 80.2293, "matched_fragments": 642, "total_fragments": 1402, "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": 79.751, "matched_fragments": 630, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Providencia sneebia", "strain": "strain=DSM 19967", "accession": "GCA_000314895.2", "taxid": 516075, "species_taxid": 516075, "relation_to_type": "type", "validated": true, "ani": 79.7036, "matched_fragments": 513, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photorhabdus temperata", "strain": "strain=DSM 14550", "accession": "GCA_025384845.1", "taxid": 574560, "species_taxid": 574560, "relation_to_type": "type", "validated": true, "ani": 78.2448, "matched_fragments": 172, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photorhabdus kayaii", "strain": "strain=DSM 15194", "accession": "GCA_025384895.1", "taxid": 230088, "species_taxid": 230088, "relation_to_type": "type", "validated": true, "ani": 78.1774, "matched_fragments": 166, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photorhabdus kleinii", "strain": "strain=DSM 23513", "accession": "GCA_025384885.1", "taxid": 768034, "species_taxid": 768034, "relation_to_type": "type", "validated": true, "ani": 77.989, "matched_fragments": 172, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photobacterium phosphoreum", "strain": "strain=ATCC 11040", "accession": "GCA_000949955.1", "taxid": 659, "species_taxid": 659, "relation_to_type": "type", "validated": true, "ani": 76.4298, "matched_fragments": 54, "total_fragments": 1402, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017151615.1", "gtdb_species": "s__Providencia stuartii_C", "ani": 95.8811, "matched_fragments": 1281, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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"min_intra_species_ani": "96.33", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000527275.1", "gtdb_species": "s__Providencia alcalifaciens_A", "ani": 80.982, "matched_fragments": 710, "total_fragments": 1402, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Providencia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.68", "min_intra_species_ani": "97.24", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 15, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.245, "cell_length": 0.33, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 39.0, "optimum_ph": 7.0, "genome_size": 3809110.876, "gc_content": 39.705, "coding_genes": 3964.9, "rRNA16S_genes": 7.0, "tRNA_genes": 77.276, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 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