{ "type": "genome", "identifier": "GCF_014268615.1", "organism": "Pseudomonas tehranensis", "title": "Pseudomonas tehranensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "KU Leuven", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014268615.1", "bioproject": "PRJNA224116", "biosample": "SAMN15248340", "wgs_master": "JABWQV000000000.1", "refseq_category": "reference genome", "taxid": "2745502", "species_taxid": "2745502", "organism_name": "Pseudomonas tehranensis", "infraspecific_name": "strain=SWRI196", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/23", "asm_name": "ASM1426861v1", "asm_submitter": "KU Leuven", "gbrs_paired_asm": "GCA_014268615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/268/615/GCF_014268615.1_ASM1426861v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5993891", "genome_size_ungapped": "5993891", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "531", "contig_count": "531", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014268615.1-RS_2024_07_22", "annotation_date": "2024-07-22", "total_gene_count": "5493", "protein_coding_gene_count": "5364", "non_coding_gene_count": "57", "pubmed_id": "32752051" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-23", "dateModified": "2020-08-23", "datePublished": "2020-08-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas tehranensis" ], "sample_taxid": [ "2745502" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Iran: Tehran" ], "sample_host_location_id": [], "data_size": "1.693 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)": "5993891", "Number of Sequences": "531", "Longest Sequences (bp)": "258826", "N50 (bp)": "21387", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.5", "Number of CDSs": "5351", "Average Protein Length": "325.3", "Coding Ratio (%)": "87.1", "Number of rRNAs": "4", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas tehranensis", "strain": "strain=SWRI196", "accession": "GCA_014268615.1", "taxid": 2745502, "species_taxid": 2745502, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1728, "total_fragments": 1747, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas rhizophila", "strain": "strain=S211", "accession": "GCA_003033885.1", "taxid": 2045200, "species_taxid": 2045200, "relation_to_type": "type", "validated": true, "ani": 94.9482, "matched_fragments": 1553, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas viciae", "strain": "strain=11K1", "accession": "GCA_004786035.1", "taxid": 2505979, "species_taxid": 2505979, "relation_to_type": "type", "validated": true, "ani": 88.6493, "matched_fragments": 1423, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kilonensis", "strain": "strain=DSM 13647", "accession": "GCA_001269885.1", "taxid": 132476, "species_taxid": 132476, "relation_to_type": "type", "validated": true, "ani": 88.3726, "matched_fragments": 1417, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicacearum", "strain": "strain=JCM 11938", "accession": "GCA_012034345.1", "taxid": 930166, "species_taxid": 930166, "relation_to_type": "suspected-type", "validated": true, "ani": 88.3262, "matched_fragments": 1457, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas bijieensis", "strain": "strain=L22-9", "accession": "GCA_013347965.1", "taxid": 2681983, "species_taxid": 2681983, "relation_to_type": "type", "validated": true, "ani": 88.3094, "matched_fragments": 1447, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicacearum subsp. brassicacearum", "strain": "strain=CCUG 51508", "accession": "GCA_008801605.1", "taxid": 86264, "species_taxid": 930166, "relation_to_type": "type", "validated": true, "ani": 88.308, "matched_fragments": 1464, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas zanjanensis", "strain": "strain=SWRI12", "accession": "GCA_014268745.2", "taxid": 2745496, "species_taxid": 2745496, "relation_to_type": "type", "validated": true, "ani": 87.8684, "matched_fragments": 1385, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sputi", "strain": "strain=BML-PP014", "accession": "GCA_021603585.1", "taxid": 2892325, "species_taxid": 2892325, "relation_to_type": "type", "validated": true, "ani": 84.0523, "matched_fragments": 1100, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pharyngis", "strain": "strain=BML-PP036", "accession": "GCA_021602345.1", "taxid": 2892333, "species_taxid": 2892333, "relation_to_type": "type", "validated": true, "ani": 83.9101, "matched_fragments": 1117, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lurida", "strain": "strain=LMG 21995", "accession": "GCA_002563895.1", "taxid": 244566, "species_taxid": 244566, "relation_to_type": "type", "validated": true, "ani": 82.8718, "matched_fragments": 990, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicae", "strain": "strain=MAFF 212427", "accession": "GCA_010671725.1", "taxid": 2708063, "species_taxid": 2708063, "relation_to_type": "type", "validated": true, "ani": 81.8041, "matched_fragments": 713, "total_fragments": 1747, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900113505.1", "gtdb_species": "s__Pseudomonas_E sp900113505", "ani": 98.134, "matched_fragments": 1599, "total_fragments": 1747, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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"min_intra_species_ani": "95.64", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_008801605.1", "gtdb_species": "s__Pseudomonas_E brassicacearum", "ani": 88.3023, "matched_fragments": 1465, "total_fragments": 1747, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.86", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_001307275.1", "gtdb_species": "s__Pseudomonas_E fluorescens_AA", "ani": 88.2979, "matched_fragments": 1446, "total_fragments": 1747, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.99", 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"min_intra_species_ani": "95.56", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "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", "tehranensis" ], "quality": 4, "quality_label": 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