{ "type": "genome", "identifier": "GCF_900109175.1", "organism": "Pseudomonas linyingensis", "title": "Pseudomonas linyingensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900109175.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216201", "wgs_master": "FNZE00000000.1", "refseq_category": "reference genome", "taxid": "915471", "species_taxid": "915471", "organism_name": "Pseudomonas linyingensis", "infraspecific_name": "strain=LMG 25967", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2663762776 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900109175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/109/175/GCF_900109175.1_IMG-taxon_2663762776_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": "4721122", "genome_size_ungapped": "4718048", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900109175.1-RS_2024_04_24", "annotation_date": "2024-04-24", "total_gene_count": "4449", "protein_coding_gene_count": "4318", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas linyingensis" ], "sample_taxid": [ "915471" ], "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": "1.289 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)": "4721122", "Number of Sequences": "43", "Longest Sequences (bp)": "467980", "N50 (bp)": "231539", "Gap Ratio (%)": "0.065112", "GCcontent (%)": "66.4", "Number of CDSs": "4332", "Average Protein Length": "322.4", "Coding Ratio (%)": "88.8", "Number of rRNAs": "7", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas linyingensis", "strain": "strain=LMG 25967", "accession": "GCA_900109175.1", 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"matched_fragments": 823, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas thermotolerans", "strain": "strain=DSM 14292", "accession": "GCA_000364625.1", "taxid": 157784, "species_taxid": 157784, "relation_to_type": "type", "validated": true, "ani": 83.2011, "matched_fragments": 731, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas insulae", "strain": "strain=UL073", "accession": "GCA_016901015.1", "taxid": 2809017, "species_taxid": 2809017, "relation_to_type": "type", "validated": true, "ani": 82.7491, "matched_fragments": 776, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas flexibilis", "strain": "strain=ATCC 29606", "accession": "GCA_900155995.1", "taxid": 706570, "species_taxid": 706570, "relation_to_type": "type", "validated": true, "ani": 82.6934, "matched_fragments": 662, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=FDAARGOS_876", "accession": "GCA_016028635.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "suspected-type", "validated": true, "ani": 82.0837, "matched_fragments": 694, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mangiferae", "strain": "strain=DMKU BBB3-04", "accession": "GCA_007109405.1", "taxid": 2593654, "species_taxid": 2593654, "relation_to_type": "type", "validated": true, "ani": 81.7529, "matched_fragments": 690, "total_fragments": 1552, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oryzihabitans", "strain": "strain=DSM 6835", "accession": "GCA_012986195.1", "taxid": 47885, "species_taxid": 47885, "relation_to_type": "suspected-type", "validated": true, "ani": 80.9524, "matched_fragments": 608, "total_fragments": 1552, "ani_threshold": 95, 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87.8987, "matched_fragments": 824, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.99", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009363155.1", "gtdb_species": "s__Azotobacter salinestris", "ani": 82.9848, "matched_fragments": 816, "total_fragments": 1552, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter", "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_000412695.1", "gtdb_species": "s__Pseudomonas_F resinovorans_A", "ani": 82.4113, 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"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", "linyingensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }