{ "type": "genome", "identifier": "GCF_012034345.1", "organism": "Pseudomonas brassicacearum", "title": "Pseudomonas brassicacearum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "China Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012034345.1", "bioproject": "PRJNA224116", "biosample": "SAMN14437789", "wgs_master": "JAATHE000000000.1", "refseq_category": "na", "taxid": "930166", "species_taxid": "930166", "organism_name": "Pseudomonas brassicacearum", "infraspecific_name": "strain=JCM 11938", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/05", "asm_name": "ASM1203434v1", "asm_submitter": "China Agricultural University", "gbrs_paired_asm": "GCA_012034345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/034/345/GCF_012034345.1_ASM1203434v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6735827", "genome_size_ungapped": "6735635", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "91", "contig_count": "91", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_012034345.1-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "6079", "protein_coding_gene_count": "5938", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-05", "dateModified": "2020-04-05", "datePublished": "2020-04-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas brassicacearum" ], "sample_taxid": [ "930166" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France" ], "sample_host_location_id": [], "data_size": "1.885 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)": "6735827", "Number of Sequences": "91", "Longest Sequences (bp)": "1280443", "N50 (bp)": "262220", "Gap Ratio (%)": "0.002850", "GCcontent (%)": "60.8", "Number of CDSs": "5943", "Average Protein Length": "329.1", "Coding Ratio (%)": "87.1", "Number of rRNAs": "4", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 2217, "total_fragments": 2219, "ani_threshold": 95, "status": "conclusive" }, { "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": 99.9966, "matched_fragments": 2210, "total_fragments": 2219, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas kilonensis", "strain": "strain=DSM 13647", "accession": "GCA_001269885.1", "taxid": 132476, "species_taxid": 132476, "relation_to_type": "type", "validated": true, "ani": 94.9309, "matched_fragments": 1839, "total_fragments": 2219, "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": 92.2994, "matched_fragments": 1898, "total_fragments": 2219, "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": 92.2355, "matched_fragments": 1873, "total_fragments": 2219, "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": 91.7782, "matched_fragments": 1736, "total_fragments": 2219, "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": 88.7017, "matched_fragments": 1684, "total_fragments": 2219, "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": 84.5961, "matched_fragments": 1353, "total_fragments": 2219, "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": 84.5833, "matched_fragments": 1321, "total_fragments": 2219, "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": 83.7755, "matched_fragments": 1320, "total_fragments": 2219, "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": 83.4332, "matched_fragments": 1220, "total_fragments": 2219, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008801605.1", "gtdb_species": "s__Pseudomonas_E brassicacearum", "ani": 99.9966, "matched_fragments": 2210, "total_fragments": 2219, "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": "conclusive" }, { "accession": "GCF_001269885.1", "gtdb_species": "s__Pseudomonas_E kilonensis", "ani": 94.9355, "matched_fragments": 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"total_fragments": 2219, "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_018325905.1", "gtdb_species": "s__Pseudomonas_E sp018325905", "ani": 93.8864, "matched_fragments": 1855, "total_fragments": 2219, "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_900581005.1", "gtdb_species": "s__Pseudomonas_E sp900581005", "ani": 92.4756, "matched_fragments": 1811, 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"total_fragments": 2219, "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": "98.81", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.0, "optimum_tmp": 26.0, "optimum_ph": 7.258, "genome_size": 6721860.333, "gc_content": 60.75, "coding_genes": 5881.0, "rRNA16S_genes": 5.0, "tRNA_genes": 65.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "brassicacearum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }