{ "type": "genome", "identifier": "GCF_003385555.1", "organism": "Rhodosalinus sediminis", "title": "Rhodosalinus sediminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shandong University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003385555.1", "bioproject": "PRJNA224116", "biosample": "SAMN09522149", "wgs_master": "QOHR00000000.1", "refseq_category": "reference genome", "taxid": "1940533", "species_taxid": "1940533", "organism_name": "Rhodosalinus sediminis", "infraspecific_name": "strain=WDN1C137", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/14", "asm_name": "ASM338555v1", "asm_submitter": "Shandong University", "gbrs_paired_asm": "GCA_003385555.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/385/555/GCF_003385555.1_ASM338555v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3156146", "genome_size_ungapped": "3155743", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "124", "contig_count": "124", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003385555.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3125", "protein_coding_gene_count": "3014", "non_coding_gene_count": "51", "pubmed_id": "29043957" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-14", "dateModified": "2018-08-14", "datePublished": "2018-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodosalinus sediminis" ], "sample_taxid": [ "1940533" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Weihai" ], "sample_host_location_id": [], "data_size": "0.842 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)": "3156146", "Number of Sequences": "124", "Longest Sequences (bp)": "381874", "N50 (bp)": "112421", "Gap Ratio (%)": "0.014131", "GCcontent (%)": "71.6", "Number of CDSs": "3013", "Average Protein Length": "305.7", "Coding Ratio (%)": "87.6", "Number of rRNAs": "2", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseivivax isoporae", "strain": "strain=LMG 25204", "accession": "GCA_000521865.1", "taxid": 591206, "species_taxid": 591206, "relation_to_type": "type", "validated": true, "ani": 79.9203, "matched_fragments": 601, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax halodurans", "strain": "strain=JCM 10272", "accession": "GCA_000521785.1", "taxid": 93683, "species_taxid": 93683, "relation_to_type": "type", "validated": true, "ani": 79.6166, "matched_fragments": 519, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limimaricola pyoseonensis", "strain": "strain=DSM 21424", "accession": "GCA_900102015.1", "taxid": 521013, "species_taxid": 521013, "relation_to_type": "type", "validated": true, "ani": 79.5749, "matched_fragments": 548, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger profundus", "strain": "strain=CGMCC 1.12377", "accession": "GCA_014637265.1", "taxid": 1229727, "species_taxid": 1229727, "relation_to_type": "type", "validated": true, "ani": 79.4749, "matched_fragments": 523, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax marinus", "strain": "strain=DSM 27511", "accession": "GCA_900109705.1", "taxid": 1379903, "species_taxid": 1379903, "relation_to_type": "type", "validated": true, "ani": 79.3555, "matched_fragments": 504, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax jejudonensis", "strain": "strain=CECT 8625", "accession": "GCA_900172265.1", "taxid": 1529041, "species_taxid": 1529041, "relation_to_type": "type", "validated": true, "ani": 79.3169, "matched_fragments": 537, "total_fragments": 1007, "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": 79.2011, "matched_fragments": 553, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salipiger thiooxidans", "strain": "strain=DSM 10146", "accession": "GCA_900102075.1", "taxid": 282683, "species_taxid": 282683, "relation_to_type": "type", "validated": true, "ani": 79.1119, "matched_fragments": 560, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Wenxinia saemankumensis", "strain": "strain=DSM 100565", "accession": "GCA_900141735.1", "taxid": 1447782, "species_taxid": 1447782, "relation_to_type": "type", "validated": true, "ani": 79.0065, "matched_fragments": 495, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allosediminivita pacifica", "strain": "strain=CGMCC 1.12410", "accession": "GCA_014637495.1", "taxid": 1267769, "species_taxid": 1267769, "relation_to_type": "type", "validated": true, "ani": 78.9779, "matched_fragments": 494, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoroseicyclus aestuarii", "strain": "strain=CECT 9025", "accession": "GCA_003217255.1", "taxid": 1795041, "species_taxid": 1795041, "relation_to_type": "type", "validated": true, "ani": 78.7892, "matched_fragments": 423, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubellimicrobium roseum", "strain": "strain=YIM 48858", "accession": "GCA_006152145.1", "taxid": 687525, "species_taxid": 687525, "relation_to_type": "type", "validated": true, "ani": 78.6409, "matched_fragments": 421, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jannaschia marina", "strain": "strain=SHC163", "accession": "GCA_013404595.1", "taxid": 2741674, "species_taxid": 2741674, "relation_to_type": "type", "validated": true, "ani": 78.6337, "matched_fragments": 450, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum euryhalinum", "strain": "strain=DSM 4868", "accession": "GCA_004342445.1", "taxid": 35805, "species_taxid": 35805, "relation_to_type": "type", "validated": true, "ani": 78.5957, "matched_fragments": 442, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseivivax halotolerans", "strain": "strain=JCM 10271", "accession": "GCA_900115815.1", "taxid": 93684, "species_taxid": 93684, "relation_to_type": "type", "validated": true, "ani": 78.4751, "matched_fragments": 422, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius indicus", "strain": "strain=DSM 26383", "accession": "GCA_900112725.1", "taxid": 540747, "species_taxid": 540747, "relation_to_type": "type", "validated": true, "ani": 78.4379, "matched_fragments": 470, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoroseicyclus tamaricis", "strain": "strain=CLL3-39", "accession": "GCA_010435925.1", "taxid": 2705421, "species_taxid": 2705421, "relation_to_type": "type", "validated": true, "ani": 78.4127, "matched_fragments": 481, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halovulum dunhuangense", "strain": "strain=YYQ-30", "accession": "GCA_013093415.1", "taxid": 1505036, "species_taxid": 1505036, "relation_to_type": "type", "validated": true, "ani": 78.4008, "matched_fragments": 390, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sinirhodobacter hankyongi", "strain": "strain=BO-81", "accession": "GCA_003664585.1", "taxid": 2294033, "species_taxid": 2294033, "relation_to_type": "type", "validated": true, "ani": 78.3961, "matched_fragments": 454, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius indicus", "strain": "strain=DSM 26383", "accession": "GCA_008728195.1", "taxid": 540747, "species_taxid": 540747, "relation_to_type": "type", "validated": true, "ani": 78.3955, "matched_fragments": 474, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rubellimicrobium aerolatum", "strain": "strain=DSM 19297", "accession": "GCA_017872975.1", "taxid": 490979, "species_taxid": 490979, "relation_to_type": "type", "validated": true, "ani": 78.3739, "matched_fragments": 427, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halovulum marinum", "strain": "strain=2CG4", "accession": "GCA_009697225.1", "taxid": 2662447, "species_taxid": 2662447, "relation_to_type": "type", "validated": true, "ani": 78.3623, "matched_fragments": 459, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum tesquicola", "strain": "strain=A-36s", "accession": "GCA_024128855.1", "taxid": 540254, "species_taxid": 540254, "relation_to_type": "type", "validated": true, "ani": 78.3542, "matched_fragments": 470, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseovarius indicus", "strain": "strain=B108", "accession": "GCA_001441635.1", "taxid": 540747, "species_taxid": 540747, "relation_to_type": "type", "validated": true, "ani": 78.3436, "matched_fragments": 484, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovulum strictum", "strain": "strain=DSM 11289", "accession": "GCA_009649175.1", "taxid": 58314, "species_taxid": 58314, "relation_to_type": "type", "validated": true, "ani": 78.2171, "matched_fragments": 435, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Palleronia rufa", "strain": "strain=MOLA 401", "accession": "GCA_000743715.1", "taxid": 1530186, "species_taxid": 1530186, "relation_to_type": "type", "validated": true, "ani": 78.0512, "matched_fragments": 352, "total_fragments": 1007, "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": 77.7551, "matched_fragments": 379, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus mutanolyticus", "strain": "strain=RSP-02", "accession": "GCA_003285265.1", "taxid": 1499308, "species_taxid": 1499308, "relation_to_type": "type", "validated": true, "ani": 77.5534, "matched_fragments": 327, "total_fragments": 1007, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003385555.1", "gtdb_species": "s__Rhodosalinus sediminis", "ani": 100.0, "matched_fragments": 1004, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus", "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_003298775.1", "gtdb_species": "s__Rhodosalinus sp003298775", "ani": 85.6078, "matched_fragments": 792, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus", "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_000521865.1", "gtdb_species": "s__Roseivivax isoporae", "ani": 79.9339, "matched_fragments": 599, "total_fragments": 1007, "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_002834145.1", "gtdb_species": "s__Roseovarius salinarum", "ani": 79.7164, "matched_fragments": 522, "total_fragments": 1007, "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_900102015.1", "gtdb_species": "s__Limimaricola pyoseonensis", "ani": 79.5289, "matched_fragments": 553, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola", "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_002166865.1", "gtdb_species": "s__Roseovarius sp002166865", "ani": 79.4974, "matched_fragments": 536, "total_fragments": 1007, "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_000153305.1", "gtdb_species": "s__Oceanicola granulosus", "ani": 79.4407, "matched_fragments": 538, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola", "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_018139985.1", "gtdb_species": "s__JAGSOU01 sp018139985", "ani": 79.4052, "matched_fragments": 543, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01", "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_900172265.1", "gtdb_species": "s__Roseivivax jejudonensis", "ani": 79.3226, "matched_fragments": 537, "total_fragments": 1007, "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_008710275.1", "gtdb_species": "s__Oceanicola sp008710275", "ani": 79.2753, "matched_fragments": 478, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola", "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_900112685.1", "gtdb_species": "s__Roseivivax sediminis", "ani": 79.2608, "matched_fragments": 535, "total_fragments": 1007, "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_900156805.1", "gtdb_species": "s__Roseivivax lentus", "ani": 79.1915, "matched_fragments": 554, "total_fragments": 1007, "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_003789055.1", "gtdb_species": "s__Oceanicola lentulus", "ani": 79.1097, "matched_fragments": 531, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola", "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_900141735.1", "gtdb_species": "s__Wenxinia saemankumensis", "ani": 79.0113, "matched_fragments": 494, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia", "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_001975705.1", "gtdb_species": "s__Salipiger abyssi", "ani": 78.6577, "matched_fragments": 497, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger", "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_002967695.1", "gtdb_species": "s__Rhodobaculum sp002967695", "ani": 78.4784, "matched_fragments": 438, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum", "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_017916275.1", "gtdb_species": "s__Rubellimicrobium sp017916275", "ani": 78.1806, "matched_fragments": 355, "total_fragments": 1007, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "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": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Rhodosalinus", "sediminis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }