{ "type": "genome", "identifier": "GCF_003033885.1", "organism": "Pseudomonas rhizophila", "title": "Pseudomonas rhizophila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Laboratoire de Biotechnologie et de Valorisation des Bioressources", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003033885.1", "bioproject": "PRJNA224116", "biosample": "SAMN07783793", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2045200", "species_taxid": "2045200", "organism_name": "Pseudomonas rhizophila", "infraspecific_name": "strain=S211", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/04", "asm_name": "ASM303388v1", "asm_submitter": "Laboratoire de Biotechnologie et de Valorisation des Bioressources", "gbrs_paired_asm": "GCA_003033885.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/033/885/GCF_003033885.1_ASM303388v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5948615", "genome_size_ungapped": "5947615", "gc_percent": "60.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003033885.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5367", "protein_coding_gene_count": "5222", "non_coding_gene_count": "69", "pubmed_id": "29527191" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-04", "dateModified": "2018-04-04", "datePublished": "2018-04-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas rhizophila" ], "sample_taxid": [ "2045200" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tunisia: Ariana, sidi thabet" ], "sample_host_location_id": [], "data_size": "1.663 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)": "5948515", "Number of Sequences": "1", "Longest Sequences (bp)": "5948515", "N50 (bp)": "5948515", "Gap Ratio (%)": "0.015130", "GCcontent (%)": "60.4", "Number of CDSs": "5266", "Average Protein Length": "331.8", "Coding Ratio (%)": "88.1", "Number of rRNAs": "8", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas rhizophila", "strain": "strain=S211", "accession": "GCA_003033885.1", "taxid": 2045200, "species_taxid": 2045200, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1981, "total_fragments": 1982, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas tehranensis", "strain": "strain=SWRI196", "accession": "GCA_014268615.1", "taxid": 2745502, "species_taxid": 2745502, "relation_to_type": "type", "validated": true, "ani": 94.8575, "matched_fragments": 1514, "total_fragments": 1982, "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": 89.1838, "matched_fragments": 1642, "total_fragments": 1982, "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": 88.7984, "matched_fragments": 1612, "total_fragments": 1982, "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": 88.7913, "matched_fragments": 1667, "total_fragments": 1982, "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": 88.7836, "matched_fragments": 1677, "total_fragments": 1982, "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": 88.5797, "matched_fragments": 1666, "total_fragments": 1982, "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": 84.1326, "matched_fragments": 1281, "total_fragments": 1982, "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": 84.0614, "matched_fragments": 1301, "total_fragments": 1982, "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": 83.3984, "matched_fragments": 1257, "total_fragments": 1982, "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": 81.7568, "matched_fragments": 830, "total_fragments": 1982, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003033885.1", "gtdb_species": "s__Pseudomonas_E sp003033885", "ani": 100.0, "matched_fragments": 1981, "total_fragments": 1982, "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": "conclusive" }, { "accession": "GCF_900113505.1", "gtdb_species": "s__Pseudomonas_E sp900113505", "ani": 94.9654, "matched_fragments": 1775, "total_fragments": 1982, "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": "-" }, { "accession": "GCF_004786035.1", "gtdb_species": "s__Pseudomonas_E viciae", "ani": 89.1741, "matched_fragments": 1643, "total_fragments": 1982, "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_001269885.1", "gtdb_species": "s__Pseudomonas_E kilonensis", "ani": 88.8053, "matched_fragments": 1611, "total_fragments": 1982, "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": 88.7897, "matched_fragments": 1676, "total_fragments": 1982, "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_000585995.1", 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"gtdb_species": "s__Pseudomonas_E kilonensis_B", "ani": 88.7272, "matched_fragments": 1673, "total_fragments": 1982, "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_900581005.1", "gtdb_species": "s__Pseudomonas_E sp900581005", "ani": 88.6164, "matched_fragments": 1634, "total_fragments": 1982, "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_013347965.1", "gtdb_species": 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