{ "type": "genome", "identifier": "GCF_001908095.1", "organism": "Xenorhabdus thuongxuanensis", "title": "Xenorhabdus thuongxuanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Goethe University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001908095.1", "bioproject": "PRJNA224116", "biosample": "SAMN05375129", "wgs_master": "MKGR00000000.1", "refseq_category": "reference genome", "taxid": "1873484", "species_taxid": "1873484", "organism_name": "Xenorhabdus thuongxuanensis", "infraspecific_name": "strain=30TX1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/19", "asm_name": "ASM190809v1", "asm_submitter": "Goethe University", "gbrs_paired_asm": "GCA_001908095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/908/095/GCF_001908095.1_ASM190809v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3938299", "genome_size_ungapped": "3935399", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "130", "contig_count": "130", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001908095.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "3650", "protein_coding_gene_count": "3381", "non_coding_gene_count": "98", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-19", "dateModified": "2016-12-19", "datePublished": "2016-12-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Xenorhabdus thuongxuanensis" ], "sample_taxid": [ "1873484" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.124 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3938299", "Number of Sequences": "130", "Longest Sequences (bp)": "336111", "N50 (bp)": "119455", "Gap Ratio (%)": "0.073636", "GCcontent (%)": "43.0", "Number of CDSs": "3446", "Average Protein Length": "315.7", "Coding Ratio (%)": "82.9", "Number of rRNAs": "6", "Number of tRNAs": "75", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xenorhabdus thuongxuanensis", "strain": "strain=30TX1", "accession": "GCA_001908095.1", "taxid": 1873484, "species_taxid": 1873484, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1261, "total_fragments": 1265, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xenorhabdus ehlersii", "strain": "strain=DSM 16337", "accession": "GCA_002632445.1", "taxid": 290111, "species_taxid": 290111, "relation_to_type": "type", "validated": true, "ani": 93.5953, "matched_fragments": 1021, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus ehlersii", "strain": "strain=DSM 16337", "accession": "GCA_003610465.1", "taxid": 290111, "species_taxid": 290111, "relation_to_type": "type", "validated": true, "ani": 93.5661, "matched_fragments": 1030, "total_fragments": 1265, "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": 93.1087, "matched_fragments": 967, "total_fragments": 1265, "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": 92.0231, "matched_fragments": 966, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus kozodoii", "strain": "strain=DSM 17907", "accession": "GCA_002632875.1", "taxid": 351676, "species_taxid": 351676, "relation_to_type": "type", "validated": true, "ani": 87.4726, "matched_fragments": 941, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus lircayensis", "strain": "strain=VLS", "accession": "GCA_016306625.1", "taxid": 2763499, "species_taxid": 2763499, "relation_to_type": "type", "validated": true, "ani": 84.7108, "matched_fragments": 884, "total_fragments": 1265, "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": 81.978, "matched_fragments": 758, "total_fragments": 1265, "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": 79.0868, "matched_fragments": 366, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 78.2187, "matched_fragments": 103, "total_fragments": 1265, "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": 77.9091, "matched_fragments": 163, "total_fragments": 1265, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001908095.1", "gtdb_species": "s__Xenorhabdus thuongxuanensis", "ani": 100.0, "matched_fragments": 1259, "total_fragments": 1265, "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": "conclusive" }, { "accession": "GCF_003610465.1", "gtdb_species": "s__Xenorhabdus ehlersii", "ani": 93.5965, "matched_fragments": 1028, "total_fragments": 1265, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001908105.1", "gtdb_species": "s__Xenorhabdus eapokensis", "ani": 93.0949, "matched_fragments": 970, "total_fragments": 1265, "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_002632755.1", "gtdb_species": "s__Xenorhabdus ishibashii", "ani": 92.0236, "matched_fragments": 966, "total_fragments": 1265, "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": 91.3054, "matched_fragments": 983, "total_fragments": 1265, "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": 90.4602, "matched_fragments": 951, "total_fragments": 1265, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.236, "cell_length": 0.444, "doubling_h": null, "growth_tmp": 25.0, "optimum_tmp": 30.0, "optimum_ph": 7.2, "genome_size": 4305586.484, "gc_content": 44.612, "coding_genes": 3821.286, "rRNA16S_genes": 7.0, "tRNA_genes": 79.6, "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", "thuongxuanensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }