{ "type": "genome", "identifier": "GCF_003940825.1", "organism": "Pseudomonas oryziphila", "title": "Pseudomonas oryziphila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shanghai JiaoTong University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003940825.1", "bioproject": "PRJNA224116", "biosample": "SAMN10524910", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2894079", "species_taxid": "2894079", "organism_name": "Pseudomonas oryziphila", "infraspecific_name": "strain=1257", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/12", "asm_name": "ASM394082v1", "asm_submitter": "Shanghai JiaoTong University", "gbrs_paired_asm": "GCA_003940825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/940/825/GCF_003940825.1_ASM394082v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6049604", "genome_size_ungapped": "6049604", "gc_percent": "64.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003940825.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5566", "protein_coding_gene_count": "5352", "non_coding_gene_count": "102", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-12", "dateModified": "2018-12-12", "datePublished": "2018-12-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas oryziphila" ], "sample_taxid": [ "2894079" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:shanghai" ], "sample_host_location_id": [], "data_size": "1.665 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)": "6049604", "Number of Sequences": "1", "Longest Sequences (bp)": "6049604", "N50 (bp)": "6049604", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.8", "Number of CDSs": "5437", "Average Protein Length": "326.8", "Coding Ratio (%)": "88.1", "Number of rRNAs": "22", "Number of tRNAs": "76", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas oryziphila", "strain": "strain=1257", "accession": "GCA_003940825.1", "taxid": 2894079, "species_taxid": 2894079, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2016, "total_fragments": 2016, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas sichuanensis", "strain": "strain=WCHPs060039", "accession": "GCA_003231305.1", "taxid": 2213015, "species_taxid": 2213015, "relation_to_type": "type", "validated": true, "ani": 96.2454, "matched_fragments": 1663, "total_fragments": 2016, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas muyukensis", "strain": "strain=COW39", "accession": "GCA_019139535.1", "taxid": 2842357, "species_taxid": 2842357, "relation_to_type": "type", "validated": true, "ani": 88.989, "matched_fragments": 1451, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas entomophila", "strain": "strain=L48", "accession": "GCA_000026105.1", "taxid": 312306, "species_taxid": 312306, "relation_to_type": "suspected-type", "validated": true, "ani": 88.9005, "matched_fragments": 1533, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas maumuensis", "strain": "strain=COW77", "accession": "GCA_019139675.1", "taxid": 2842354, "species_taxid": 2842354, "relation_to_type": "type", "validated": true, "ani": 88.8984, "matched_fragments": 1438, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_019823065.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 88.865, "matched_fragments": 1462, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_000621225.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 88.7666, "matched_fragments": 1459, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas soli", "strain": "strain=LMG 27941", "accession": "GCA_900110655.1", "taxid": 1306993, "species_taxid": 1306993, "relation_to_type": "type", "validated": true, "ani": 88.6718, "matched_fragments": 1405, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_013373935.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 87.7968, "matched_fragments": 1299, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_021602585.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 87.7065, "matched_fragments": 1381, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_021602465.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 86.6371, "matched_fragments": 1373, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_022548835.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 86.5817, "matched_fragments": 1285, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_013373915.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 86.5591, "matched_fragments": 1338, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas ceruminis", "strain": "strain=BML-PP028", "accession": "GCA_013373895.1", "taxid": 2740516, "species_taxid": 2740516, 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"ani": 77.1465, "matched_fragments": 189, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter algicola", "strain": "strain=DG893", "accession": "GCA_000170835.1", "taxid": 236100, "species_taxid": 236100, "relation_to_type": "type", "validated": true, "ani": 76.727, "matched_fragments": 91, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Seongchinamella unica", "strain": "strain=GH4-78", "accession": "GCA_004354085.1", "taxid": 2547392, "species_taxid": 2547392, "relation_to_type": "type", "validated": true, "ani": 75.9922, "matched_fragments": 119, "total_fragments": 2016, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella laticis", "strain": "strain=SAP-17", "accession": "GCA_015644585.1", "taxid": 2787622, "species_taxid": 2787622, "relation_to_type": "type", "validated": true, "ani": 75.6611, "matched_fragments": 61, "total_fragments": 2016, 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"mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.767, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 5663774.24, "gc_content": 60.938, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "range_salinity": 0.666, "facultative_respiration": 0.021, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.978, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 0.988, "coccus_cell_shape": 0.011, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "oryziphila" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }