{ "type": "genome", "identifier": "GCF_004342065.1", "organism": "Primorskyibacter sedentarius", "title": "Primorskyibacter sedentarius", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004342065.1", "bioproject": "PRJNA224116", "biosample": "SAMN10362855", "wgs_master": "SLZU00000000.1", "refseq_category": "reference genome", "taxid": "745311", "species_taxid": "745311", "organism_name": "Primorskyibacter sedentarius", "infraspecific_name": "strain=DSM 104836", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM434206v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004342065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/342/065/GCF_004342065.1_ASM434206v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5069498", "genome_size_ungapped": "5069498", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "85", "contig_count": "85", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004342065.1-RS_2024_04_17", "annotation_date": "2024-04-17", "total_gene_count": "4740", "protein_coding_gene_count": "4593", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Primorskyibacter sedentarius" ], "sample_taxid": [ "745311" ], "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": "1.426 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)": "5069498", "Number of Sequences": "85", "Longest Sequences (bp)": "823326", "N50 (bp)": "188077", "Gap Ratio (%)": "0.000158", "GCcontent (%)": "60.8", "Number of CDSs": "4692", "Average Protein Length": "317.1", "Coding Ratio (%)": "88.1", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Primorskyibacter sedentarius", "strain": "strain=DSM 104836", "accession": "GCA_004342065.1", "taxid": 745311, "species_taxid": 745311, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1645, "total_fragments": 1647, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Primorskyibacter marinus", "strain": "strain=PX7", "accession": "GCA_003313245.1", "taxid": 1977320, "species_taxid": 1977320, "relation_to_type": "type", "validated": true, "ani": 81.9742, "matched_fragments": 791, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger marinus", "strain": "strain=DSM 26424", "accession": "GCA_900100085.1", "taxid": 555512, "species_taxid": 555512, "relation_to_type": "type", "validated": true, "ani": 78.5242, "matched_fragments": 538, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria intermedia", "strain": "strain=DSM 29341", "accession": "GCA_900129345.1", "taxid": 996115, "species_taxid": 996115, "relation_to_type": "type", "validated": true, "ani": 78.3274, "matched_fragments": 443, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mameliella alba", "strain": "strain=DSM 26384", "accession": "GCA_003051025.1", "taxid": 561184, "species_taxid": 561184, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2899, "matched_fragments": 518, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mameliella alba", "strain": "strain=CGMCC 1.7290", "accession": "GCA_900101505.1", "taxid": 561184, "species_taxid": 561184, "relation_to_type": "suspected-type", "validated": true, "ani": 78.2393, "matched_fragments": 529, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Poseidonocella pacifica", "strain": "strain=DSM 29316", "accession": "GCA_900111875.1", "taxid": 871651, "species_taxid": 871651, "relation_to_type": "type", "validated": true, "ani": 78.1425, "matched_fragments": 275, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cribrihabitans marinus", "strain": "strain=DSM 29340", "accession": "GCA_900109035.1", "taxid": 1227549, "species_taxid": 1227549, "relation_to_type": "type", "validated": true, "ani": 78.1253, "matched_fragments": 449, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cribrihabitans marinus", "strain": "strain=CGMCC 1.13219", "accession": "GCA_014640375.1", "taxid": 1227549, "species_taxid": 1227549, "relation_to_type": "type", "validated": true, "ani": 78.0967, "matched_fragments": 452, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marivita lacus", "strain": "strain=CGMCC 1.12478", "accession": "GCA_014637725.1", "taxid": 1323742, "species_taxid": 1323742, "relation_to_type": "type", "validated": true, "ani": 78.0879, "matched_fragments": 470, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thalassobius aquimarinus", "strain": "strain=KMM 8518", "accession": "GCA_018219815.1", "taxid": 2785917, "species_taxid": 2785917, "relation_to_type": "type", "validated": true, "ani": 78.0106, "matched_fragments": 428, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax lentus", "strain": "strain=DSM 29430", "accession": "GCA_900156805.1", "taxid": 633194, "species_taxid": 633194, "relation_to_type": "type", "validated": true, "ani": 78.0039, "matched_fragments": 427, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudooceanicola aestuarii", "strain": "strain=E2-1", "accession": "GCA_010614805.1", "taxid": 2697319, "species_taxid": 2697319, "relation_to_type": "type", "validated": true, "ani": 77.9792, "matched_fragments": 378, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagivirga sediminicola", "strain": "strain=BH-SD19", "accession": "GCA_003072125.1", "taxid": 2170575, "species_taxid": 2170575, "relation_to_type": "type", "validated": true, "ani": 77.9134, "matched_fragments": 389, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger bermudensis", "strain": "strain=HTCC2601", "accession": "GCA_000153725.1", "taxid": 344736, "species_taxid": 344736, "relation_to_type": "type", "validated": true, "ani": 77.9036, "matched_fragments": 467, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudosulfitobacter pseudonitzschiae", "strain": "strain=DSM 26824", "accession": "GCA_900129395.1", "taxid": 1402135, "species_taxid": 1402135, "relation_to_type": "type", "validated": true, "ani": 77.8897, "matched_fragments": 412, "total_fragments": 1647, "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": 77.8649, "matched_fragments": 413, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ruegeria sediminis", "strain": "strain=CAU 1488", "accession": "GCA_005938215.1", "taxid": 2583820, "species_taxid": 2583820, "relation_to_type": "type", "validated": true, "ani": 77.8607, "matched_fragments": 397, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger pallidus", "strain": "strain=CGMCC 1.15762", "accession": "GCA_014643635.1", "taxid": 1775170, "species_taxid": 1775170, "relation_to_type": "type", "validated": true, "ani": 77.6571, "matched_fragments": 346, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax isoporae", "strain": "strain=LMG 25204", "accession": "GCA_000521865.1", "taxid": 591206, "species_taxid": 591206, "relation_to_type": "type", "validated": true, "ani": 77.5689, "matched_fragments": 356, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Falsiruegeria mediterranea", "strain": "strain=CECT 7615", "accession": "GCA_900302455.1", "taxid": 1280832, "species_taxid": 1280832, "relation_to_type": "type", "validated": true, "ani": 77.3914, "matched_fragments": 319, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseobacter cerasinus", "strain": "strain=AI77", "accession": "GCA_009811755.1", "taxid": 2602289, "species_taxid": 2602289, "relation_to_type": "type", "validated": true, "ani": 77.3844, "matched_fragments": 325, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sulfitobacter noctilucae", "strain": "strain=NB-68", "accession": "GCA_000622365.1", "taxid": 1342302, "species_taxid": 1342302, "relation_to_type": "type", "validated": true, "ani": 77.1739, "matched_fragments": 273, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 77.1402, "matched_fragments": 304, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 77.1313, "matched_fragments": 305, "total_fragments": 1647, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004342065.1", "gtdb_species": "s__Primorskyibacter sedentarius", "ani": 100.0, "matched_fragments": 1645, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter", "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": "conclusive" }, { "accession": "GCF_003313245.1", "gtdb_species": "s__Primorskyibacter marinus", "ani": 81.9734, "matched_fragments": 792, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter", "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_900176485.1", "gtdb_species": "s__Primorskyibacter flagellatus_A", "ani": 81.9009, "matched_fragments": 830, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter", "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_019104745.1", "gtdb_species": "s__CAU-1522 sp019104745", "ani": 78.5558, "matched_fragments": 501, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522", "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_900101505.1", "gtdb_species": "s__Mameliella alba", "ani": 78.2496, "matched_fragments": 529, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.14", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_900111875.1", "gtdb_species": "s__Poseidonocella pacifica", "ani": 78.1563, "matched_fragments": 274, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella", "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_900184945.1", "gtdb_species": "s__Maliponia aquimaris", "ani": 78.1469, "matched_fragments": 522, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia", "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_900109035.1", "gtdb_species": "s__Cribrihabitans marinus", "ani": 78.1257, "matched_fragments": 449, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014637725.1", "gtdb_species": "s__Marivita lacus", "ani": 78.0925, "matched_fragments": 471, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita", "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_002210095.1", "gtdb_species": "s__Marinibacterium profundimaris", "ani": 78.0334, "matched_fragments": 485, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium", "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_900156805.1", "gtdb_species": "s__Roseivivax lentus", "ani": 78.0125, "matched_fragments": 426, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax", "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_000620505.1", "gtdb_species": "s__Ascidiaceihabitans sp000620505", "ani": 77.9386, "matched_fragments": 414, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "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_900129395.1", "gtdb_species": "s__Ascidiaceihabitans pseudonitzschiae", "ani": 77.9053, "matched_fragments": 410, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013031405.1", "gtdb_species": "s__Ruegeria sp013031405", "ani": 77.8543, "matched_fragments": 453, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria", "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_003260265.1", "gtdb_species": "s__Roseovarius sp003260265", "ani": 77.7921, "matched_fragments": 359, "total_fragments": 1647, "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_002222635.1", "gtdb_species": "s__Ascidiaceihabitans pseudonitzschiae_A", "ani": 77.4927, "matched_fragments": 342, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.92", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900302455.1", "gtdb_species": "s__Ruegeria_E mediterranea", "ani": 77.3932, "matched_fragments": 319, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009811755.1", "gtdb_species": "s__Roseobacter cerasinus", "ani": 77.3923, "matched_fragments": 324, "total_fragments": 1647, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Primorskyibacter", "sedentarius" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }