{ "type": "genome", "identifier": "GCF_900099945.1", "organism": "Pseudomonas delhiensis", "title": "Pseudomonas delhiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900099945.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216189", "wgs_master": "FNEC00000000.1", "refseq_category": "na", "taxid": "366289", "species_taxid": "366289", "organism_name": "Pseudomonas delhiensis", "infraspecific_name": "strain=CCM 7361", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/21", "asm_name": "IMG-taxon 2671180033 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900099945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/099/945/GCF_900099945.1_IMG-taxon_2671180033_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6710571", "genome_size_ungapped": "6707277", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "101", "contig_count": "101", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900099945.1-RS_2024_04_21", "annotation_date": "2024-04-21", "total_gene_count": "6020", "protein_coding_gene_count": "5871", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-21", "dateModified": "2016-10-21", "datePublished": "2016-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas delhiensis" ], "sample_taxid": [ "366289" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.814 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)": "6710571", "Number of Sequences": "101", "Longest Sequences (bp)": "295316", "N50 (bp)": "125662", "Gap Ratio (%)": "0.049087", "GCcontent (%)": "68.1", "Number of CDSs": "5936", "Average Protein Length": "326.5", "Coding Ratio (%)": "86.6", "Number of rRNAs": "5", "Number of tRNAs": "61", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas delhiensis", "strain": "strain=CCM 7361", "accession": "GCA_900099945.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2180, "total_fragments": 2187, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=RLD-1", "accession": "GCA_900187975.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 99.9906, "matched_fragments": 2161, "total_fragments": 2187, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=LMG 18378", "accession": "GCA_900112375.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 95.13, "matched_fragments": 1900, "total_fragments": 2187, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=DSM 50332", "accession": "GCA_004745455.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", 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"total_fragments": 2187, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cavernae", "strain": "strain=K2W31S-8", "accession": "GCA_003595175.1", "taxid": 2320867, "species_taxid": 2320867, "relation_to_type": "type", "validated": true, "ani": 83.2166, "matched_fragments": 1029, "total_fragments": 2187, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 82.9786, "matched_fragments": 1045, "total_fragments": 2187, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 82.8897, "matched_fragments": 832, "total_fragments": 2187, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900187975.1", "gtdb_species": "s__Pseudomonas delhiensis", "ani": 99.9906, "matched_fragments": 2161, "total_fragments": 2187, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.078, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "inconclusive" }, { "accession": "GCF_900112375.1", "gtdb_species": "s__Pseudomonas citronellolis", "ani": 95.138, "matched_fragments": 1899, "total_fragments": 2187, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.078, "mean_intra_species_ani": "97.44", 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"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_017491605.1", "gtdb_species": "s__Pseudomonas sp017491605", "ani": 87.2297, "matched_fragments": 1411, "total_fragments": 2187, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_000349845.1", "gtdb_species": "s__Pseudomonas sp000349845", "ani": 87.2122, "matched_fragments": 1419, "total_fragments": 2187, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", 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"N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_017589465.1", "gtdb_species": "s__Pseudomonas sp017589465", "ani": 86.325, "matched_fragments": 1278, "total_fragments": 2187, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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": -0.302, "cell_length": 0.176, "doubling_h": -0.025, "growth_tmp": 33.0, "optimum_tmp": 37.0, "optimum_ph": 7.258, "genome_size": 6719000.5, "gc_content": 60.938, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, 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