{ "type": "genome", "identifier": "GCF_000280765.1", "organism": "Pseudomonas gingeri NCPPB 3146 = LMG 5327", "title": "Pseudomonas gingeri NCPPB 3146 = LMG 5327", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Oxford", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000280765.1", "bioproject": "PRJNA224116", "biosample": "SAMN02471742", "wgs_master": "AKBP00000000.1", "refseq_category": "na", "taxid": "707248", "species_taxid": "117681", "organism_name": "Pseudomonas gingeri NCPPB 3146 = LMG 5327", "infraspecific_name": "strain=NCPPB 3146", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/07/30", "asm_name": "ASM28076v1", "asm_submitter": "University of Oxford", "gbrs_paired_asm": "GCA_000280765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/280/765/GCF_000280765.1_ASM28076v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7666642", "genome_size_ungapped": "7571741", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "75", "contig_count": "1036", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000280765.1-RS_2024_03_30", "annotation_date": "2024-03-30", "total_gene_count": "7350", "protein_coding_gene_count": "7068", "non_coding_gene_count": "49", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-07-30", "dateModified": "2012-07-30", "datePublished": "2012-07-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas gingeri NCPPB 3146 = LMG 5327" ], "sample_taxid": [ "707248" ], "sample_host_organism": [ "Agaricus bisporus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "2.118 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)": "7666642", "Number of Sequences": "75", "Longest Sequences (bp)": "699925", "N50 (bp)": "253573", "Gap Ratio (%)": "1.237843", "GCcontent (%)": "62.6", "Number of CDSs": "6784", "Average Protein Length": "324.1", "Coding Ratio (%)": "86.0", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas agarici", "strain": "strain=LMG 2112", "accession": "GCA_900109755.1", "taxid": 46677, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_021602465.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 81.8756, "matched_fragments": 1031, "total_fragments": 2524, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_013373915.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 81.8468, "matched_fragments": 1005, "total_fragments": 2524, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas baltica", "strain": "strain=MBT-2", "accession": "GCA_014235765.1", "taxid": 2762576, "species_taxid": 2762576, "relation_to_type": "type", "validated": true, "ani": 81.7094, "matched_fragments": 832, "total_fragments": 2524, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013386115.1", "gtdb_species": "s__Pseudomonas_E gingeri_B", "ani": 98.7691, "matched_fragments": 2306, "total_fragments": 2524, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.43", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "conclusive" }, { "accession": "GCF_013385635.1", "gtdb_species": "s__Pseudomonas_E gingeri_A", "ani": 93.8105, "matched_fragments": 2208, "total_fragments": 2524, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.63", 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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_000820515.1", "gtdb_species": "s__Pseudomonas_E batumici", "ani": 87.0256, "matched_fragments": 1481, "total_fragments": 2524, "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_900105475.1", "gtdb_species": "s__Pseudomonas_E asplenii", "ani": 86.9632, "matched_fragments": 1604, "total_fragments": 2524, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": 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