{ "type": "genome", "identifier": "GCF_009756665.1", "organism": "Permianibacter aggregans", "title": "Permianibacter aggregans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shantou University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009756665.1", "bioproject": "PRJNA224116", "biosample": "SAMN11110836", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1510150", "species_taxid": "1510150", "organism_name": "Permianibacter aggregans", "infraspecific_name": "strain=HW001", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/12/16", "asm_name": "ASM975666v1", "asm_submitter": "Shantou University", "gbrs_paired_asm": "GCA_009756665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/756/665/GCF_009756665.1_ASM975666v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4266648", "genome_size_ungapped": "4266648", "gc_percent": "54.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009756665.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "3845", "protein_coding_gene_count": "3753", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-12-16", "dateModified": "2019-12-16", "datePublished": "2019-12-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Permianibacter aggregans" ], "sample_taxid": [ "1510150" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: TX, Imperial" ], "sample_host_location_id": [], "data_size": "1.197 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)": "4266648", "Number of Sequences": "1", "Longest Sequences (bp)": "4266648", "N50 (bp)": "4266648", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.4", "Number of CDSs": "3823", "Average Protein Length": "332.4", "Coding Ratio (%)": "89.3", "Number of rRNAs": "6", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Permianibacter aggregans", "strain": "strain=HW001", "accession": "GCA_009756665.1", "taxid": 1510150, "species_taxid": 1510150, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1420, "total_fragments": 1422, "ani_threshold": 95, 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"Saccharospirillum mangrovi", "strain": "strain=HK-33", "accession": "GCA_003367315.1", "taxid": 2161747, "species_taxid": 2161747, "relation_to_type": "type", "validated": true, "ani": 76.6609, "matched_fragments": 51, "total_fragments": 1422, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alcanivorax pacificus", "strain": "strain=W11-5", "accession": "GCA_000299335.2", "taxid": 1306787, "species_taxid": 1306787, "relation_to_type": "type", "validated": true, "ani": 76.3511, "matched_fragments": 54, "total_fragments": 1422, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharospirillum mangrovi", "strain": "strain=HK-33", "accession": "GCA_003054775.1", "taxid": 2161747, "species_taxid": 2161747, "relation_to_type": "type", "validated": true, "ani": 76.3372, "matched_fragments": 50, "total_fragments": 1422, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas syringae group genomosp. 7", "strain": "strain=ICMP 4091", "accession": "GCA_022557255.1", "taxid": 251699, "species_taxid": 251699, "relation_to_type": "pathovar", "validated": true, "ani": 76.1178, "matched_fragments": 59, "total_fragments": 1422, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus nantongensis", "strain": "strain=X1", "accession": "GCA_001598055.1", "taxid": 1796606, "species_taxid": 1796606, "relation_to_type": "type", "validated": true, "ani": 76.1161, "matched_fragments": 53, "total_fragments": 1422, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas syringae group genomosp. 7", "strain": "strain=ICMP 4091", "accession": "GCA_001401315.1", "taxid": 251699, "species_taxid": 251699, "relation_to_type": "pathovar", "validated": true, "ani": 75.5313, "matched_fragments": 54, "total_fragments": 1422, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, 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"accession": "GCF_001598055.1", "gtdb_species": "s__Cupriavidus nantongensis", "ani": 76.3585, "matched_fragments": 55, "total_fragments": 1422, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.73", "min_intra_species_ani": "95.73", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.78", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000299335.2", "gtdb_species": "s__Alcanivorax_A pacificus", "ani": 76.295, "matched_fragments": 54, "total_fragments": 1422, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A", "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_002087235.1", "gtdb_species": "s__Pseudomonas_E floridensis", "ani": 76.0767, "matched_fragments": 56, "total_fragments": 1422, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_002803095.1", "gtdb_species": "s__Pseudomonas_E sp002803095", "ani": 75.786, "matched_fragments": 61, "total_fragments": 1422, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.6432, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013522825.1", "gtdb_species": "s__Pseudomonas_A stutzeri_AK", "ani": 75.7501, "matched_fragments": 54, "total_fragments": 1422, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "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": "GCA_013284265.1", "gtdb_species": "s__Rugamonas sp013284265", "ani": 75.3167, "matched_fragments": 55, "total_fragments": 1422, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Permianibacter", "aggregans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }