{ "type": "genome", "identifier": "GCF_900187975.1", "organism": "Pseudomonas delhiensis", "title": "Pseudomonas delhiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900187975.1", "bioproject": "PRJNA224116", "biosample": "SAMN06295949", "wgs_master": "FZPC00000000.1", "refseq_category": "reference genome", "taxid": "366289", "species_taxid": "366289", "organism_name": "Pseudomonas delhiensis", "infraspecific_name": "strain=RLD-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/07/16", "asm_name": "IMG-taxon 2706795031 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900187975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/187/975/GCF_900187975.1_IMG-taxon_2706795031_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": "6727430", "genome_size_ungapped": "6727430", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "81", "contig_count": "81", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900187975.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "6015", "protein_coding_gene_count": "5873", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-07-16", "dateModified": "2017-07-16", "datePublished": "2017-07-16", "_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)": "6727430", "Number of Sequences": "81", "Longest Sequences (bp)": "426943", "N50 (bp)": "168606", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.1", "Number of CDSs": "5958", "Average Protein Length": "326.7", "Coding Ratio (%)": "86.8", "Number of rRNAs": "3", "Number of tRNAs": "64", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas delhiensis", "strain": "strain=RLD-1", "accession": "GCA_900187975.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2202, "total_fragments": 2204, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=CCM 7361", "accession": "GCA_900099945.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 99.985, "matched_fragments": 2169, "total_fragments": 2204, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas citronellolis", "strain": "strain=NBRC 103043", "accession": "GCA_002091555.1", "taxid": 53408, "species_taxid": 53408, "relation_to_type": "type", "validated": true, "ani": 95.0574, "matched_fragments": 1895, "total_fragments": 2204, "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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"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": 100.0, "matched_fragments": 2202, "total_fragments": 2204, "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": "conclusive" }, { "accession": "GCF_900112375.1", "gtdb_species": "s__Pseudomonas citronellolis", "ani": 95.0435, "matched_fragments": 1929, "total_fragments": 2204, "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_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_016919445.1", "gtdb_species": "s__Pseudomonas sp016919445", "ani": 86.3367, "matched_fragments": 1485, "total_fragments": 2204, "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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