{ "type": "genome", "identifier": "GCF_003610015.1", "organism": "Zymobacter palmae", "title": "Zymobacter palmae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Tottori University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003610015.1", "bioproject": "PRJNA224116", "biosample": "SAMD00136070", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "33074", "species_taxid": "33074", "organism_name": "Zymobacter palmae", "infraspecific_name": "strain=IAM14233", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/09/12", "asm_name": "ASM361001v1", "asm_submitter": "Tottori University", "gbrs_paired_asm": "GCA_003610015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/610/015/GCF_003610015.1_ASM361001v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3028543", "genome_size_ungapped": "3028543", "gc_percent": "56.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003610015.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "2696", "protein_coding_gene_count": "2581", "non_coding_gene_count": "103", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-09-12", "dateModified": "2018-09-12", "datePublished": "2018-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Zymobacter palmae" ], "sample_taxid": [ "33074" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "0.856 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)": "3028543", "Number of Sequences": "2", "Longest Sequences (bp)": "3023483", "N50 (bp)": "3023483", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.1", "Number of CDSs": "2650", "Average Protein Length": "309.7", "Coding Ratio (%)": "81.3", "Number of rRNAs": "24", "Number of tRNAs": "76", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Zymobacter palmae", "strain": "strain=IAM14233", "accession": "GCA_003610015.1", "taxid": 33074, "species_taxid": 33074, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1008, "total_fragments": 1008, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Zymobacter palmae", "strain": "strain=DSM 10491", "accession": "GCA_000620025.1", "taxid": 33074, "species_taxid": 33074, "relation_to_type": "type", "validated": true, "ani": 99.9465, "matched_fragments": 961, "total_fragments": 1008, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas meridiana", "strain": "strain=ACAM 246", "accession": "GCA_900129255.1", "taxid": 29570, "species_taxid": 29570, "relation_to_type": "type", "validated": true, "ani": 79.3465, "matched_fragments": 68, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas sulfidoxydans", "strain": "strain=MCCC 1A11059", "accession": "GCA_017868775.1", "taxid": 2733484, "species_taxid": 2733484, "relation_to_type": "type", "validated": true, "ani": 78.4771, "matched_fragments": 86, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas huangheensis", "strain": "strain=BJGMM-B45", "accession": "GCA_001431725.1", "taxid": 1178482, "species_taxid": 1178482, "relation_to_type": "type", "validated": true, "ani": 78.3122, "matched_fragments": 80, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas meridiana", "strain": "strain=NBRC 15608", "accession": "GCA_006540125.1", "taxid": 29570, "species_taxid": 29570, "relation_to_type": "type", "validated": true, "ani": 77.8496, "matched_fragments": 60, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cobetia marina", "strain": "strain=JCM 21022", "accession": "GCA_001720485.1", "taxid": 28258, "species_taxid": 28258, "relation_to_type": "type", "validated": true, "ani": 77.829, "matched_fragments": 129, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aquamarina", "strain": "strain=558", "accession": "GCA_900110265.1", "taxid": 77097, "species_taxid": 77097, "relation_to_type": "type", "validated": true, "ani": 77.5984, "matched_fragments": 61, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas bachuensis", "strain": "strain=DX6", "accession": "GCA_011742165.1", "taxid": 2717286, "species_taxid": 2717286, "relation_to_type": "type", "validated": true, "ani": 77.4952, "matched_fragments": 74, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas songnenensis", "strain": "strain=CGMCC 1.12152", "accession": "GCA_003002925.1", "taxid": 1176243, "species_taxid": 1176243, "relation_to_type": "type", "validated": true, "ani": 77.3738, "matched_fragments": 79, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=FDAARGOS_877", "accession": "GCA_016028515.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 77.3412, "matched_fragments": 75, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas campisalis", "strain": "strain=A4", "accession": "GCA_022341425.1", "taxid": 74661, "species_taxid": 74661, "relation_to_type": "type", "validated": true, "ani": 77.2558, "matched_fragments": 72, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinicola aestuarinus", "strain": "strain=CPA62", "accession": "GCA_003206645.1", "taxid": 1949082, "species_taxid": 1949082, "relation_to_type": "type", "validated": true, "ani": 77.1026, "matched_fragments": 88, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas smyrnensis", "strain": "strain=AAD6", "accession": "GCA_000265245.2", "taxid": 720605, "species_taxid": 720605, "relation_to_type": "type", "validated": true, "ani": 77.0586, "matched_fragments": 91, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria phyllosphaerae", "strain": "strain=EAod3", "accession": "GCA_900312995.1", "taxid": 2100822, "species_taxid": 2100822, "relation_to_type": "type", "validated": true, "ani": 76.8638, "matched_fragments": 85, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas gudaonensis", "strain": "strain=CGMCC 1.6133", "accession": "GCA_900100195.1", "taxid": 376427, "species_taxid": 376427, "relation_to_type": "type", "validated": true, "ani": 76.6775, "matched_fragments": 86, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lysinitropha", "strain": "strain=3(2)", "accession": "GCA_902500215.1", "taxid": 2607506, "species_taxid": 2607506, "relation_to_type": "type", "validated": true, "ani": 76.6576, "matched_fragments": 69, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria sinocarnis", "strain": "strain=DSM 23229", "accession": "GCA_003633775.1", "taxid": 595502, "species_taxid": 595502, "relation_to_type": "type", "validated": true, "ani": 76.5374, "matched_fragments": 88, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_900167195.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 76.0104, "matched_fragments": 59, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=DNSP21", "accession": "GCA_002890935.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 75.9426, "matched_fragments": 66, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003610015.1", "gtdb_species": "s__Zymobacter palmae", "ani": 100.0, "matched_fragments": 1005, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Zymobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_012427705.1", "gtdb_species": "s__Halomonas piezotolerans", "ani": 79.1144, "matched_fragments": 78, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000196875.2", "gtdb_species": "s__Halomonas elongata", "ani": 78.3308, "matched_fragments": 90, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.56", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001431725.1", "gtdb_species": "s__Halomonas huangheensis", "ani": 78.2831, "matched_fragments": 80, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001886615.1", "gtdb_species": "s__Halomonas aestuarii", "ani": 78.2739, "matched_fragments": 83, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_900155385.1", "gtdb_species": "s__Halomonas massiliensis", "ani": 78.1827, "matched_fragments": 53, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013407925.2", "gtdb_species": "s__Pseudomonas_E fluorescens_AP", "ani": 77.9291, "matched_fragments": 61, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001720485.1", "gtdb_species": "s__Cobetia marina", "ani": 77.7202, "matched_fragments": 128, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.31", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_900110265.1", "gtdb_species": "s__Halomonas aquamarina", 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"total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_001457615.1", "gtdb_species": "s__Pseudomonas aeruginosa", "ani": 77.3424, "matched_fragments": 66, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "97.38", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.84", "num_clustered_genomes": 5623, "status": "-" }, { "accession": "GCF_008298015.1", "gtdb_species": "s__Salinicola sp008298015", "ani": 77.2362, "matched_fragments": 73, "total_fragments": 1008, 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"d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C", "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_013009075.1", "gtdb_species": "s__Halomonas_B sp013009075", "ani": 77.1041, "matched_fragments": 89, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014651775.1", "gtdb_species": "s__Halomonas hamiltonii", "ani": 77.072, "matched_fragments": 83, "total_fragments": 1008, "gtdb_taxonomy": 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