{ "type": "genome", "identifier": "GCF_000319305.2", "organism": "Pseudomonas bharatica CSV86", "title": "Pseudomonas bharatica CSV86", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Environmental Engineering Research Institute (NEERI)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000319305.2", "bioproject": "PRJNA224116", "biosample": "SAMN02472262", "wgs_master": "AMWJ00000000.2", "refseq_category": "reference genome", "taxid": "1005395", "species_taxid": "2692112", "organism_name": "Pseudomonas bharatica CSV86", "infraspecific_name": "strain=CSV86", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/11", "asm_name": "ASM31930v2", "asm_submitter": "National Environmental Engineering Research Institute (NEERI)", "gbrs_paired_asm": "GCA_000319305.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/319/305/GCF_000319305.2_ASM31930v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6787172", "genome_size_ungapped": "6787172", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000319305.2-RS_2024_09_27", "annotation_date": "2024-09-27", "total_gene_count": "6435", "protein_coding_gene_count": "5650", "non_coding_gene_count": "96", "pubmed_id": "23469351" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-11", "dateModified": "2020-05-11", "datePublished": "2020-05-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas bharatica CSV86" ], "sample_taxid": [ "1005395" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Bangalore" ], "sample_host_location_id": [], "data_size": "1.868 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 79.46, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6787172", "Number of Sequences": "9", "Longest Sequences (bp)": "3033951", "N50 (bp)": "2711763", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.7", "Number of CDSs": "6621", "Average Protein Length": "299.0", "Coding Ratio (%)": "87.5", "Number of rRNAs": "19", "Number of tRNAs": "75", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas bharatica", "strain": "strain=CSV86", "accession": "GCA_000319305.2", "taxid": 2692112, "species_taxid": 2692112, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2251, "total_fragments": 2258, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas japonica", "strain": "strain=NBRC 103040", "accession": "GCA_000730585.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 88.262, "matched_fragments": 1490, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas japonica", "strain": "strain=DSM 22348", "accession": "GCA_900188455.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 88.1673, "matched_fragments": 1547, "total_fragments": 2258, "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": 84.3058, "matched_fragments": 1200, "total_fragments": 2258, "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": 84.3029, "matched_fragments": 1135, "total_fragments": 2258, "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": 84.2168, "matched_fragments": 1006, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alkylphenolica", "strain": "strain=KL28", "accession": "GCA_000746525.1", "taxid": 237609, "species_taxid": 237609, "relation_to_type": "type", "validated": true, "ani": 83.9441, "matched_fragments": 1128, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas vranovensis", "strain": "strain=DSM 16006", "accession": "GCA_000425805.1", "taxid": 321661, "species_taxid": 321661, "relation_to_type": "type", "validated": true, "ani": 83.5904, "matched_fragments": 1154, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas putida", "strain": "strain=ATCC 12633", "accession": "GCA_024508115.1", "taxid": 303, "species_taxid": 303, "relation_to_type": "suspected-type", "validated": true, "ani": 83.3473, "matched_fragments": 1234, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sessilinigenes", "strain": "strain=CMR12a", "accession": "GCA_019139855.1", "taxid": 658629, "species_taxid": 658629, "relation_to_type": "type", "validated": true, "ani": 82.2877, "matched_fragments": 1096, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas arcuscaelestis", "strain": "strain=P66", "accession": "GCA_016881005.1", "taxid": 2710591, "species_taxid": 2710591, "relation_to_type": "type", "validated": true, "ani": 81.9274, "matched_fragments": 1020, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 81.8118, "matched_fragments": 803, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salsipaludibacter albus", "strain": "strain=AS10", "accession": "GCA_019798055.1", "taxid": 2849650, "species_taxid": 2849650, "relation_to_type": "type", "validated": true, "ani": 75.0763, "matched_fragments": 74, "total_fragments": 2258, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.46, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000319305.2", "gtdb_species": "s__Pseudomonas_E putida_C", "ani": 100.0, "matched_fragments": 2251, "total_fragments": 2258, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.35", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001941965.1", "gtdb_species": "s__Pseudomonas_E putida_L", "ani": 91.0842, "matched_fragments": 1789, "total_fragments": 2258, "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_003523465.1", "gtdb_species": "s__Pseudomonas_E sp003523465", "ani": 89.5301, "matched_fragments": 696, "total_fragments": 2258, "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_900188455.1", "gtdb_species": "s__Pseudomonas_E japonica", "ani": 88.1762, "matched_fragments": 1546, "total_fragments": 2258, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900187455.1", "gtdb_species": "s__Pseudomonas_E sp900187455", "ani": 86.7707, "matched_fragments": 1586, "total_fragments": 2258, "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_003231275.1", "gtdb_species": "s__Pseudomonas_E huaxiensis", "ani": 86.4744, "matched_fragments": 1548, "total_fragments": 2258, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.93", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018417635.1", "gtdb_species": "s__Pseudomonas_E sp900101695", "ani": 84.7472, "matched_fragments": 1261, "total_fragments": 2258, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003105155.1", "gtdb_species": "s__Pseudomonas_E sp003105155", "ani": 84.7339, "matched_fragments": 1140, "total_fragments": 2258, "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_019168305.1", "gtdb_species": "s__Pseudomonas_E sp019168305", "ani": 84.537, "matched_fragments": 1180, "total_fragments": 2258, "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_016009175.1", "gtdb_species": "s__Pseudomonas_E alkylphenolica_B", "ani": 83.4212, "matched_fragments": 1133, "total_fragments": 2258, "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": "-" } ] }, "_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", "bharatica", "CSV86" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }