{ "type": "genome", "identifier": "GCF_002632725.1", "organism": "Xenorhabdus hominickii", "title": "Xenorhabdus hominickii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Goethe University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002632725.1", "bioproject": "PRJNA224116", "biosample": "SAMN05375102", "wgs_master": "NJAI00000000.1", "refseq_category": "na", "taxid": "351679", "species_taxid": "351679", "organism_name": "Xenorhabdus hominickii", "infraspecific_name": "strain=DSM 17903", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/23", "asm_name": "ASM263272v1", "asm_submitter": "Goethe University", "gbrs_paired_asm": "GCA_002632725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/632/725/GCF_002632725.1_ASM263272v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5347057", "genome_size_ungapped": "5335857", "gc_percent": "43.500000", "replicon_count": "0", "scaffold_count": "133", "contig_count": "133", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002632725.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5083", "protein_coding_gene_count": "4690", "non_coding_gene_count": "105", "pubmed_id": "28993611" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-23", "dateModified": "2017-10-23", "datePublished": "2017-10-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Xenorhabdus hominickii" ], "sample_taxid": [ "351679" ], "sample_host_organism": [ "Steinernema karii" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Kenya" ], "sample_host_location_id": [], "data_size": "1.522 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5347057", "Number of Sequences": "133", "Longest Sequences (bp)": "1579613", "N50 (bp)": "545410", "Gap Ratio (%)": "0.209461", "GCcontent (%)": "43.4", "Number of CDSs": "4825", "Average Protein Length": "302.1", "Coding Ratio (%)": "81.8", "Number of rRNAs": "22", "Number of tRNAs": "83", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xenorhabdus hominickii", "strain": "strain=DSM 17903", "accession": "GCA_002632725.1", "taxid": 351679, "species_taxid": 351679, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1642, "total_fragments": 1737, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xenorhabdus lircayensis", "strain": "strain=VLS", "accession": "GCA_016306625.1", "taxid": 2763499, "species_taxid": 2763499, "relation_to_type": "type", "validated": true, "ani": 84.8754, "matched_fragments": 1023, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus vietnamensis", "strain": "strain=DSM 22392", "accession": "GCA_002127535.1", "taxid": 351656, "species_taxid": 351656, "relation_to_type": "type", "validated": true, "ani": 83.9319, "matched_fragments": 1004, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus japonica", "strain": "strain=DSM 16522", "accession": "GCA_900115195.1", "taxid": 53341, "species_taxid": 53341, "relation_to_type": "type", "validated": true, "ani": 83.8268, "matched_fragments": 910, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus miraniensis", "strain": "strain=DSM 17902", "accession": "GCA_002632615.1", "taxid": 351674, "species_taxid": 351674, "relation_to_type": "type", "validated": true, "ani": 83.7913, "matched_fragments": 1028, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus beddingii", "strain": "strain=DSM 4764", "accession": "GCA_002127545.1", "taxid": 40578, "species_taxid": 40578, "relation_to_type": "type", "validated": true, "ani": 83.2999, "matched_fragments": 930, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus koppenhoeferi", "strain": "strain=DSM 18168", "accession": "GCA_900116635.1", "taxid": 351659, "species_taxid": 351659, "relation_to_type": "type", "validated": true, "ani": 83.2553, "matched_fragments": 763, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus ishibashii", "strain": "strain=DSM 22670", "accession": "GCA_002632755.1", "taxid": 1034471, "species_taxid": 1034471, "relation_to_type": "type", "validated": true, "ani": 83.1792, "matched_fragments": 896, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus eapokensis", "strain": "strain=DL20", "accession": "GCA_001908105.1", "taxid": 1873482, "species_taxid": 1873482, "relation_to_type": "type", "validated": true, "ani": 83.0112, "matched_fragments": 900, "total_fragments": 1737, "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": 82.9905, "matched_fragments": 898, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus nematophila", "strain": "strain=ATCC 19061", "accession": "GCA_000252955.1", "taxid": 628, "species_taxid": 628, "relation_to_type": "type", "validated": true, "ani": 82.6929, "matched_fragments": 904, "total_fragments": 1737, "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": 79.0797, "matched_fragments": 379, "total_fragments": 1737, "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": 78.8478, "matched_fragments": 361, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yersinia aldovae", "strain": "strain=IP06005", "accession": "GCA_001091225.1", "taxid": 29483, "species_taxid": 29483, "relation_to_type": "type", "validated": true, "ani": 77.7122, "matched_fragments": 179, "total_fragments": 1737, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_002632725.1", "gtdb_species": "s__Xenorhabdus hominickii", "ani": 100.0, "matched_fragments": 1637, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_016306625.1", "gtdb_species": "s__Xenorhabdus sp016306625", "ani": 84.8968, "matched_fragments": 1022, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002127535.1", "gtdb_species": "s__Xenorhabdus vietnamensis", "ani": 83.912, "matched_fragments": 1001, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_900115195.1", "gtdb_species": "s__Xenorhabdus japonica", "ani": 83.8488, "matched_fragments": 908, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001037465.1", "gtdb_species": "s__Xenorhabdus khoisanae", "ani": 83.8188, "matched_fragments": 1020, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002632615.1", "gtdb_species": "s__Xenorhabdus miraniensis", "ani": 83.7607, "matched_fragments": 1032, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.51", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002127545.1", "gtdb_species": "s__Xenorhabdus beddingii", "ani": 83.2994, "matched_fragments": 930, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000973125.1", "gtdb_species": "s__Xenorhabdus bovienii", "ani": 83.0296, "matched_fragments": 995, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "96.37", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001908105.1", "gtdb_species": "s__Xenorhabdus eapokensis", "ani": 82.9751, "matched_fragments": 899, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_015163665.1", "gtdb_species": "s__Xenorhabdus sp015163665", "ani": 82.9099, "matched_fragments": 918, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_015163655.1", "gtdb_species": "s__Xenorhabdus griffiniae", "ani": 82.8335, "matched_fragments": 876, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001028135.1", "gtdb_species": "s__Xenorhabdus griffiniae_A", "ani": 82.7854, "matched_fragments": 896, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000252955.1", "gtdb_species": "s__Xenorhabdus nematophila", "ani": 82.6929, "matched_fragments": 907, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.26", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000027225.1", "gtdb_species": "s__Xenorhabdus bovienii_C", "ani": 82.4393, "matched_fragments": 932, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.07", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002632465.1", "gtdb_species": "s__Xenorhabdus budapestensis", "ani": 81.9569, "matched_fragments": 799, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000968175.1", "gtdb_species": "s__Xenorhabdus poinarii", "ani": 81.9313, "matched_fragments": 806, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.71", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014467235.1", "gtdb_species": "s__Xenorhabdus indica", "ani": 81.7433, "matched_fragments": 842, "total_fragments": 1737, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.18", "min_intra_species_ani": "99.18", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.236, "cell_length": 0.444, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 30.0, "optimum_ph": 7.2, "genome_size": 4522699.333, "gc_content": 43.4, "coding_genes": 3835.5, "rRNA16S_genes": 7.0, "tRNA_genes": 87.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.666, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Xenorhabdus", "hominickii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }