{ "type": "genome", "identifier": "GCF_014268805.2", "organism": "Pseudomonas farsensis", "title": "Pseudomonas farsensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "KU Leuven", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014268805.2", "bioproject": "PRJNA224116", "biosample": "SAMN15248330", "wgs_master": "JABWRF000000000.2", "refseq_category": "reference genome", "taxid": "2745492", "species_taxid": "2745492", "organism_name": "Pseudomonas farsensis", "infraspecific_name": "strain=SWRI107", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/06", "asm_name": "ASM1426880v2", "asm_submitter": "KU Leuven", "gbrs_paired_asm": "GCA_014268805.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/268/805/GCF_014268805.2_ASM1426880v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5249961", "genome_size_ungapped": "5249961", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014268805.2-RS_2024_07_22", "annotation_date": "2024-07-22", "total_gene_count": "4715", "protein_coding_gene_count": "4558", "non_coding_gene_count": "98", "pubmed_id": "32752051" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-06", "dateModified": "2021-07-06", "datePublished": "2021-07-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas farsensis" ], "sample_taxid": [ "2745492" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Iran: Shiraz" ], "sample_host_location_id": [], "data_size": "1.452 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)": "5249961", "Number of Sequences": "6", "Longest Sequences (bp)": "2087791", "N50 (bp)": "1525682", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.6", "Number of CDSs": "4665", "Average Protein Length": "331.1", "Coding Ratio (%)": "88.3", "Number of rRNAs": "19", "Number of tRNAs": "81", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas farsensis", "strain": "strain=SWRI107", "accession": "GCA_014268805.2", "taxid": 2745492, "species_taxid": 2745492, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1742, "total_fragments": 1746, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas fakonensis", "strain": "strain=COW40", "accession": "GCA_019139895.1", "taxid": 2842355, "species_taxid": 2842355, "relation_to_type": "type", "validated": true, "ani": 87.6873, "matched_fragments": 1386, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas xanthosomae", "strain": "strain=COR54", "accession": "GCA_019139835.1", "taxid": 2842356, "species_taxid": 2842356, "relation_to_type": "type", "validated": true, "ani": 87.5959, "matched_fragments": 1417, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas muyukensis", "strain": "strain=COW39", "accession": "GCA_019139535.1", "taxid": 2842357, "species_taxid": 2842357, "relation_to_type": "type", "validated": true, "ani": 86.6422, "matched_fragments": 1260, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sichuanensis", "strain": "strain=WCHPs060039", "accession": "GCA_003231305.1", "taxid": 2213015, "species_taxid": 2213015, "relation_to_type": "type", "validated": true, "ani": 86.6181, "matched_fragments": 1247, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oryziphila", "strain": "strain=1257", "accession": "GCA_003940825.1", "taxid": 2894079, "species_taxid": 2894079, "relation_to_type": "type", "validated": true, "ani": 86.6118, "matched_fragments": 1300, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas xantholysinigenes", "strain": "strain=RW9S1A", "accession": "GCA_014268885.2", "taxid": 2745490, "species_taxid": 2745490, "relation_to_type": "type", "validated": true, "ani": 86.286, "matched_fragments": 1271, "total_fragments": 1746, "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": 86.2063, "matched_fragments": 1256, "total_fragments": 1746, "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": 86.1932, "matched_fragments": 1279, "total_fragments": 1746, "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": 86.1518, "matched_fragments": 1253, "total_fragments": 1746, "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": 86.1273, "matched_fragments": 1141, "total_fragments": 1746, "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": 86.1127, "matched_fragments": 1216, "total_fragments": 1746, "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": 85.9472, "matched_fragments": 1260, "total_fragments": 1746, "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": 85.4058, "matched_fragments": 1118, "total_fragments": 1746, "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": 85.1478, "matched_fragments": 1256, "total_fragments": 1746, "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": 85.1068, "matched_fragments": 1226, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014268825.1", "gtdb_species": "s__Pseudomonas_E sp014268825", "ani": 98.641, "matched_fragments": 1541, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_019139835.1", "gtdb_species": "s__Pseudomonas_E sp019139835", "ani": 87.5795, "matched_fragments": 1417, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.50", "min_intra_species_ani": "95.50", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_019139535.1", "gtdb_species": "s__Pseudomonas_E sp019139535", "ani": 86.653, "matched_fragments": 1259, "total_fragments": 1746, "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_003231305.1", "gtdb_species": "s__Pseudomonas_E sichuanensis", "ani": 86.5989, "matched_fragments": 1250, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.11", "min_intra_species_ani": "95.79", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_015354575.1", "gtdb_species": "s__Pseudomonas_E sp015354575", "ani": 86.4291, "matched_fragments": 1286, "total_fragments": 1746, "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_016861355.1", "gtdb_species": "s__Pseudomonas_E sp001259595", "ani": 86.3994, "matched_fragments": 1278, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.3017, "mean_intra_species_ani": "95.65", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003205295.1", "gtdb_species": "s__Pseudomonas_E mosselii_B", "ani": 86.3582, "matched_fragments": 1244, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.3017, "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_004519305.1", "gtdb_species": "s__Pseudomonas_E sp004519305", "ani": 86.2427, "matched_fragments": 1214, "total_fragments": 1746, "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_019139675.1", "gtdb_species": "s__Pseudomonas_E sp019139675", "ani": 86.1714, "matched_fragments": 1256, "total_fragments": 1746, "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_013373935.1", "gtdb_species": "s__Pseudomonas_E sp002438125", "ani": 86.1269, "matched_fragments": 1140, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.14", "min_intra_species_ani": "98.14", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900110655.1", "gtdb_species": "s__Pseudomonas_E soli", "ani": 85.9403, "matched_fragments": 1261, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "95.09", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_011752565.1", "gtdb_species": "s__Pseudomonas_E sp011752565", "ani": 85.6633, "matched_fragments": 1263, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000935045.1", "gtdb_species": "s__Pseudomonas_E sp000935045", "ani": 85.5415, "matched_fragments": 1190, "total_fragments": 1746, "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_000282535.1", "gtdb_species": "s__Pseudomonas_E sp000282535", "ani": 85.4493, "matched_fragments": 1075, "total_fragments": 1746, "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_016648105.1", "gtdb_species": "s__Pseudomonas_E sp016648105", "ani": 85.2974, "matched_fragments": 1198, "total_fragments": 1746, "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": "GCA_003428805.1", "gtdb_species": "s__Pseudomonas_E sp003428805", "ani": 85.1444, "matched_fragments": 1242, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.29", "min_intra_species_ani": "96.05", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_013393325.1", "gtdb_species": "s__Pseudomonas_E putida_P", "ani": 84.9078, "matched_fragments": 1223, "total_fragments": 1746, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 10, "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", "farsensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }