{ "type": "genome", "identifier": "GCF_003254185.1", "organism": "Planktotalea frisia", "title": "Planktotalea frisia", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003254185.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660220", "wgs_master": "QKZM00000000.1", "refseq_category": "na", "taxid": "696762", "species_taxid": "696762", "organism_name": "Planktotalea frisia", "infraspecific_name": "strain=DSM 23709", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/19", "asm_name": "ASM325418v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003254185.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/185/GCF_003254185.1_ASM325418v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4159922", "genome_size_ungapped": "4158536", "gc_percent": "54.000000", "replicon_count": "0", "scaffold_count": "200", "contig_count": "200", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003254185.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "4335", "protein_coding_gene_count": "4167", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-19", "dateModified": "2018-06-19", "datePublished": "2018-06-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Planktotalea frisia" ], "sample_taxid": [ "696762" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: North Sea" ], "sample_host_location_id": [], "data_size": "1.191 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)": "4159922", "Number of Sequences": "200", "Longest Sequences (bp)": "158133", "N50 (bp)": "41424", "Gap Ratio (%)": "0.033318", "GCcontent (%)": "53.8", "Number of CDSs": "4107", "Average Protein Length": "298.5", "Coding Ratio (%)": "88.4", "Number of rRNAs": "9", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Planktotalea frisia", "strain": "strain=DSM 23709", "accession": "GCA_003254185.1", "taxid": 696762, "species_taxid": 696762, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1276, "total_fragments": 1286, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Planktotalea frisia", "strain": "strain=SH6-1", "accession": "GCA_001890925.1", "taxid": 696762, "species_taxid": 696762, "relation_to_type": "type", "validated": true, "ani": 99.9653, "matched_fragments": 1191, "total_fragments": 1286, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Cognatishimia activa", "strain": "strain=CECT 5113", "accession": "GCA_001458335.1", "taxid": 1715691, "species_taxid": 1715691, "relation_to_type": "type", "validated": true, "ani": 80.7117, "matched_fragments": 129, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Planktotalea arctica", "strain": "strain=IMCC9565", "accession": "GCA_002105285.1", "taxid": 1481893, "species_taxid": 1481893, "relation_to_type": "type", "validated": true, "ani": 79.6002, "matched_fragments": 504, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter indolifex", "strain": "strain=DSM 14862", "accession": "GCA_022788655.1", "taxid": 225422, "species_taxid": 225422, "relation_to_type": "type", "validated": true, "ani": 78.2499, "matched_fragments": 147, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter donghicola", "strain": "strain=KCTC 12864", "accession": "GCA_000622405.1", "taxid": 421000, "species_taxid": 421000, "relation_to_type": "type", "validated": true, "ani": 77.2812, "matched_fragments": 158, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alexandriicola marinus", "strain": "strain=LZ-14", "accession": "GCA_004000435.1", "taxid": 2081710, "species_taxid": 2081710, "relation_to_type": "type", "validated": true, "ani": 76.911, "matched_fragments": 71, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pacificibacter maritimus", "strain": "strain=DSM 104731", "accession": "GCA_003814915.1", "taxid": 762213, "species_taxid": 762213, "relation_to_type": "type", "validated": true, "ani": 76.8298, "matched_fragments": 89, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter donghicola", "strain": "strain=JCM 14565", "accession": "GCA_000712275.1", "taxid": 421000, "species_taxid": 421000, "relation_to_type": "type", "validated": true, "ani": 76.7821, "matched_fragments": 150, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=H3", "accession": "GCA_000712315.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 76.7236, "matched_fragments": 162, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yoonia rosea", "strain": "strain=DSM 29591", "accession": "GCA_900156505.1", "taxid": 287098, "species_taxid": 287098, "relation_to_type": "type", "validated": true, "ani": 76.6621, "matched_fragments": 132, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shimia haliotis", "strain": "strain=DSM 28453", "accession": "GCA_900114415.1", "taxid": 1280847, "species_taxid": 1280847, "relation_to_type": "type", "validated": true, "ani": 76.5606, "matched_fragments": 138, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagicola litoralis", "strain": "strain=CL-ES2", "accession": "GCA_005518135.1", "taxid": 420403, "species_taxid": 420403, "relation_to_type": "type", "validated": true, "ani": 76.4565, "matched_fragments": 108, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter dubius", "strain": "strain=DSM 16472", "accession": "GCA_900113435.1", "taxid": 218673, "species_taxid": 218673, "relation_to_type": "type", "validated": true, "ani": 76.3508, "matched_fragments": 129, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter litoreus", "strain": "strain=ASW11-22", "accession": "GCA_020165855.1", "taxid": 2876714, "species_taxid": 2876714, "relation_to_type": "type", "validated": true, "ani": 76.3051, "matched_fragments": 71, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola sediminis", "strain": "strain=DRYC-M-16", "accession": "GCA_004745575.1", "taxid": 2486418, "species_taxid": 2486418, "relation_to_type": "type", "validated": true, "ani": 76.2835, "matched_fragments": 56, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yangia pacifica", "strain": "strain=CGMCC 1.3455", "accession": "GCA_900100725.1", "taxid": 311180, "species_taxid": 311180, "relation_to_type": "suspected-type", "validated": true, "ani": 76.186, "matched_fragments": 68, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yangia pacifica", "strain": "strain=DSM 26894", "accession": "GCA_900116195.1", "taxid": 311180, "species_taxid": 311180, "relation_to_type": "suspected-type", "validated": true, "ani": 76.1129, "matched_fragments": 66, "total_fragments": 1286, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001890925.1", "gtdb_species": "s__Planktotalea frisia", "ani": 99.9653, "matched_fragments": 1191, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCA_000156115.1", "gtdb_species": "s__Planktotalea sp000156115", "ani": 80.4821, "matched_fragments": 634, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.77", "min_intra_species_ani": "99.74", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018607995.1", "gtdb_species": "s__Planktotalea sp018607995", "ani": 80.0138, "matched_fragments": 561, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea", "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_002105285.1", "gtdb_species": "s__Planktotalea arctica", "ani": 79.6106, "matched_fragments": 503, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea", "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": "GCA_018607965.1", "gtdb_species": "s__Planktotalea sp018607965", "ani": 79.2308, "matched_fragments": 481, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea", "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_011040495.1", "gtdb_species": "s__Roseovarius aestuariivivens_A", "ani": 77.1475, "matched_fragments": 101, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius", "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_900156505.1", "gtdb_species": "s__Yoonia rosea", "ani": 76.6621, "matched_fragments": 132, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.70", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017798205.1", "gtdb_species": "s__Cognatishimia activa_A", "ani": 76.4346, "matched_fragments": 155, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia", "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_001292625.1", "gtdb_species": "s__Shimia sp001292625", "ani": 76.4025, "matched_fragments": 144, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia", "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": "GCA_006226775.1", "gtdb_species": "s__Marinovum sp006226775", "ani": 76.0784, "matched_fragments": 71, "total_fragments": 1286, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum", "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": -0.26, "cell_length": 0.352, "doubling_h": null, "growth_tmp": 20.0, "optimum_tmp": 22.5, "optimum_ph": 8.25, "genome_size": 4133329.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Planktotalea", "frisia" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }