{ "type": "genome", "identifier": "GCF_019145195.1", "organism": "Pseudomonas siliginis", "title": "Pseudomonas siliginis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "KU Leuven", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019145195.1", "bioproject": "PRJNA224116", "biosample": "SAMN19473661", "wgs_master": "JAHSTW000000000.1", "refseq_category": "na", "taxid": "2842346", "species_taxid": "2842346", "organism_name": "Pseudomonas siliginis", "infraspecific_name": "strain=SWRI31", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/06", "asm_name": "ASM1914519v1", "asm_submitter": "KU Leuven", "gbrs_paired_asm": "GCA_019145195.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/145/195/GCF_019145195.1_ASM1914519v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5690467", "genome_size_ungapped": "5690467", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "51", "contig_count": "51", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019145195.1-RS_2024_07_22", "annotation_date": "2024-07-22", "total_gene_count": "5200", "protein_coding_gene_count": "5072", "non_coding_gene_count": "68", "pubmed_id": "na" }, "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 siliginis" ], "sample_taxid": [ "2842346" ], "sample_host_organism": [ "Wheat" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Iran: Kermanshah" ], "sample_host_location_id": [], "data_size": "1.589 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)": "5690467", "Number of Sequences": "51", "Longest Sequences (bp)": "884355", "N50 (bp)": "382979", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.0", "Number of CDSs": "5121", "Average Protein Length": "325.0", "Coding Ratio (%)": "87.8", "Number of rRNAs": "3", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas siliginis", "strain": "strain=SWRI31", "accession": "GCA_019145195.1", "taxid": 2842346, "species_taxid": 2842346, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1877, "total_fragments": 1878, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas atacamensis", "strain": "strain=M7D1", "accession": "GCA_004801935.1", "taxid": 2565368, "species_taxid": 2565368, "relation_to_type": "type", "validated": true, "ani": 96.138, "matched_fragments": 1706, "total_fragments": 1878, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas triticicola", "strain": "strain=SWRI88", "accession": "GCA_019145375.1", "taxid": 2842345, "species_taxid": 2842345, "relation_to_type": "type", "validated": true, "ani": 95.8057, "matched_fragments": 1661, "total_fragments": 1878, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas iranensis", "strain": "strain=SWRI54", "accession": "GCA_014268585.2", "taxid": 2745503, "species_taxid": 2745503, "relation_to_type": "type", "validated": true, "ani": 95.6783, "matched_fragments": 1714, "total_fragments": 1878, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas granadensis", "strain": "strain=LMG 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"taxid": 2745509, "species_taxid": 2745509, "relation_to_type": "type", "validated": true, "ani": 88.0083, "matched_fragments": 1538, "total_fragments": 1878, "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": 87.5966, "matched_fragments": 1438, "total_fragments": 1878, "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": 87.5799, "matched_fragments": 1486, "total_fragments": 1878, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, 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"min_intra_species_ani": "98.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900105805.1", "gtdb_species": "s__Pseudomonas_E moraviensis_A", "ani": 92.6865, "matched_fragments": 1648, "total_fragments": 1878, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002836515.1", "gtdb_species": "s__Pseudomonas_E sp002836515", "ani": 92.628, "matched_fragments": 1597, "total_fragments": 1878, "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_900105485.1", "gtdb_species": "s__Pseudomonas_E granadensis", "ani": 88.6751, "matched_fragments": 1562, "total_fragments": 1878, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.04", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_003999415.1", "gtdb_species": "s__Pseudomonas_E koreensis_E", "ani": 88.0581, "matched_fragments": 1483, "total_fragments": 1878, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000292795.1", "gtdb_species": "s__Pseudomonas_E fluorescens_H", "ani": 87.9929, "matched_fragments": 1516, "total_fragments": 1878, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "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", "siliginis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }