{ "type": "genome", "identifier": "GCF_004786035.1", "organism": "Pseudomonas viciae", "title": "Pseudomonas viciae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "China Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004786035.1", "bioproject": "PRJNA224116", "biosample": "SAMN10724295", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2505979", "species_taxid": "2505979", "organism_name": "Pseudomonas viciae", "infraspecific_name": "strain=11K1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/12", "asm_name": "ASM478603v1", "asm_submitter": "China Agricultural University", "gbrs_paired_asm": "GCA_004786035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/786/035/GCF_004786035.1_ASM478603v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6704877", "genome_size_ungapped": "6704877", "gc_percent": "60.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004786035.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5897", "protein_coding_gene_count": "5758", "non_coding_gene_count": "84", "pubmed_id": "30941113" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-12", "dateModified": "2019-04-12", "datePublished": "2019-04-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas viciae" ], "sample_taxid": [ "2505979" ], "sample_host_organism": [ "Vicia faba" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Yunnan" ], "sample_host_location_id": [], "data_size": "1.874 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)": "6704877", "Number of Sequences": "2", "Longest Sequences (bp)": "6682832", "N50 (bp)": "6682832", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.3", "Number of CDSs": "5825", "Average Protein Length": "338.3", "Coding Ratio (%)": "88.2", "Number of rRNAs": "16", "Number of tRNAs": "66", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas viciae", "strain": "strain=11K1", "accession": "GCA_004786035.1", "taxid": 2505979, "species_taxid": 2505979, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2233, "total_fragments": 2234, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas bijieensis", "strain": "strain=L22-9", "accession": "GCA_013347965.1", "taxid": 2681983, "species_taxid": 2681983, "relation_to_type": "type", "validated": true, "ani": 90.5908, "matched_fragments": 1805, "total_fragments": 2234, "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": 90.3021, "matched_fragments": 1724, "total_fragments": 2234, "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": 90.1066, "matched_fragments": 1788, "total_fragments": 2234, "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": 90.1008, "matched_fragments": 1790, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas thivervalensis", "strain": "strain=DSM 13194", "accession": "GCA_001269655.1", "taxid": 86265, "species_taxid": 86265, "relation_to_type": "type", "validated": true, "ani": 89.4698, "matched_fragments": 1753, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizophila", "strain": "strain=S211", "accession": "GCA_003033885.1", "taxid": 2045200, "species_taxid": 2045200, "relation_to_type": "type", "validated": true, "ani": 89.0812, "matched_fragments": 1651, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas tehranensis", "strain": "strain=SWRI196", "accession": "GCA_014268615.1", "taxid": 2745502, "species_taxid": 2745502, "relation_to_type": "type", "validated": true, "ani": 88.5453, "matched_fragments": 1417, "total_fragments": 2234, "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": 84.4013, "matched_fragments": 1334, "total_fragments": 2234, "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": 84.3839, "matched_fragments": 1311, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas germanica", "strain": "strain=FIT28", "accession": "GCA_019614655.1", "taxid": 2815720, "species_taxid": 2815720, "relation_to_type": "type", "validated": true, "ani": 83.7529, "matched_fragments": 1294, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, "relation_to_type": "type", "validated": true, "ani": 83.3417, "matched_fragments": 1216, "total_fragments": 2234, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004786035.1", "gtdb_species": "s__Pseudomonas_E viciae", "ani": 100.0, "matched_fragments": 2233, "total_fragments": 2234, "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": "conclusive" }, { "accession": "GCF_017968885.1", "gtdb_species": "s__Pseudomonas_E sp017968885", "ani": 92.9059, "matched_fragments": 1966, "total_fragments": 2234, "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_000585995.1", "gtdb_species": "s__Pseudomonas_E brassicacearum_A", "ani": 90.4014, "matched_fragments": 1820, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.55", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001269885.1", "gtdb_species": "s__Pseudomonas_E kilonensis", "ani": 90.2998, "matched_fragments": 1725, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.12", "min_intra_species_ani": "95.91", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_008801605.1", "gtdb_species": "s__Pseudomonas_E brassicacearum", "ani": 90.1022, "matched_fragments": 1790, "total_fragments": 2234, "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_001623525.1", "gtdb_species": "s__Pseudomonas_E fluorescens_Q", "ani": 89.9648, "matched_fragments": 1776, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "97.11", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_900581005.1", "gtdb_species": "s__Pseudomonas_E sp900581005", "ani": 89.961, "matched_fragments": 1729, "total_fragments": 2234, "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_009601685.2", "gtdb_species": "s__Pseudomonas_E kilonensis_B", "ani": 89.9555, "matched_fragments": 1774, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.30", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_018325905.1", "gtdb_species": "s__Pseudomonas_E sp018325905", "ani": 89.8308, "matched_fragments": 1753, "total_fragments": 2234, "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_001307275.1", "gtdb_species": "s__Pseudomonas_E fluorescens_AA", "ani": 89.7031, "matched_fragments": 1841, "total_fragments": 2234, "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", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_003033885.1", "gtdb_species": "s__Pseudomonas_E sp003033885", "ani": 89.0875, "matched_fragments": 1649, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_900113505.1", "gtdb_species": "s__Pseudomonas_E sp900113505", "ani": 88.7115, "matched_fragments": 1646, "total_fragments": 2234, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.10", "min_intra_species_ani": "95.53", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 12, "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", "viciae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }