{ "type": "genome", "identifier": "GCF_000515255.1", "organism": "Rhodovibrio salinarum DSM 9154", "title": "Rhodovibrio salinarum DSM 9154", "description": "na", "data type": "Genome sequencing and assembly", "organization": "JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000515255.1", "bioproject": "PRJNA224116", "biosample": "SAMN02597269", "wgs_master": "AZXM00000000.1", "refseq_category": "reference genome", "taxid": "1089552", "species_taxid": "1087", "organism_name": "Rhodovibrio salinarum DSM 9154", "infraspecific_name": "strain=DSM 9154", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/01/07", "asm_name": "ASM51525v1", "asm_submitter": "JGI", "gbrs_paired_asm": "GCA_000515255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/515/255/GCF_000515255.1_ASM51525v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4176524", "genome_size_ungapped": "4176324", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000515255.1-RS_2024_07_21", "annotation_date": "2024-07-21", "total_gene_count": "3850", "protein_coding_gene_count": "3753", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-01-07", "dateModified": "2014-01-07", "datePublished": "2014-01-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodovibrio salinarum DSM 9154" ], "sample_taxid": [ "1089552" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Portugal" ], "sample_host_location_id": [], "data_size": "1.154 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)": "4176524", "Number of Sequences": "1", "Longest Sequences (bp)": "4176524", "N50 (bp)": "4176524", "Gap Ratio (%)": "0.005196", "GCcontent (%)": "66.0", "Number of CDSs": "3843", "Average Protein Length": "318.5", "Coding Ratio (%)": "87.9", "Number of rRNAs": "4", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodovibrio salinarum", "strain": "strain=DSM 9154", "accession": "GCA_000515255.1", "taxid": 1087, "species_taxid": 1087, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1391, "total_fragments": 1392, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodovibrio salinarum", "strain": "strain=DSM 9154", "accession": "GCA_016583505.1", "taxid": 1087, "species_taxid": 1087, "relation_to_type": "type", "validated": true, "ani": 99.9745, "matched_fragments": 1360, "total_fragments": 1392, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodovibrio sodomensis", "strain": "strain=DSM 9895", "accession": "GCA_016583645.1", "taxid": 1088, "species_taxid": 1088, "relation_to_type": "type", "validated": true, "ani": 84.988, "matched_fragments": 950, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ferruginivarius sediminum", "strain": "strain=WD2A32", "accession": "GCA_003344765.1", "taxid": 2661937, "species_taxid": 2661937, "relation_to_type": "type", "validated": true, "ani": 78.6664, "matched_fragments": 405, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limimonas halophila", "strain": "strain=DSM 25584", "accession": "GCA_900100655.1", "taxid": 1082479, "species_taxid": 1082479, "relation_to_type": "type", "validated": true, "ani": 78.5466, "matched_fragments": 319, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tistlia consotensis", "strain": "strain=DSM 21585", "accession": "GCA_900188055.1", "taxid": 1321365, "species_taxid": 1321365, "relation_to_type": "type", "validated": true, "ani": 77.5117, "matched_fragments": 442, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibius marinus", "strain": "strain=NBU2595", "accession": "GCA_014925385.1", "taxid": 2762760, "species_taxid": 2762760, "relation_to_type": "type", "validated": true, "ani": 77.4104, "matched_fragments": 325, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella pratensis", "strain": "strain=W17", "accession": "GCA_008843145.1", "taxid": 2233999, "species_taxid": 2233999, "relation_to_type": "type", "validated": true, "ani": 77.3371, "matched_fragments": 275, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella stibiiresistens", "strain": "strain=SB22", "accession": "GCA_000576635.1", "taxid": 913326, "species_taxid": 913326, "relation_to_type": "type", "validated": true, "ani": 76.9578, "matched_fragments": 270, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Algihabitans albus", "strain": "strain=HHTR 118", "accession": "GCA_003572205.1", "taxid": 2164067, "species_taxid": 2164067, "relation_to_type": "type", "validated": true, "ani": 76.8026, "matched_fragments": 201, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nisaea acidiphila", "strain": "strain=MEBiC11861", "accession": "GCA_024662015.1", "taxid": 1862145, "species_taxid": 1862145, "relation_to_type": "type", "validated": true, "ani": 76.7889, "matched_fragments": 161, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Minwuia thermotolerans", "strain": "strain=SY3-15", "accession": "GCA_002924445.1", "taxid": 2056226, "species_taxid": 2056226, "relation_to_type": "type", "validated": true, "ani": 76.7583, "matched_fragments": 209, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vineibacter terrae", "strain": "strain=CC-CFT640", "accession": "GCA_008039615.1", "taxid": 2586908, "species_taxid": 2586908, "relation_to_type": "type", "validated": true, "ani": 76.644, "matched_fragments": 258, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas haemaphysalidis", "strain": "strain=546", "accession": "GCA_017355405.1", "taxid": 2768162, "species_taxid": 2768162, "relation_to_type": "type", "validated": true, "ani": 76.6335, "matched_fragments": 164, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Reyranella aquatilis", "strain": "strain=KCTC 52223", "accession": "GCA_020880995.1", "taxid": 2035356, "species_taxid": 2035356, "relation_to_type": "type", "validated": true, "ani": 76.6009, "matched_fragments": 201, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000515255.1", "gtdb_species": "s__Rhodovibrio salinarum", "ani": 100.0, "matched_fragments": 1391, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio", "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": "conclusive" }, { "accession": "GCF_016583645.1", "gtdb_species": "s__Rhodovibrio sodomensis", "ani": 84.9906, "matched_fragments": 948, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio", "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_003344765.1", "gtdb_species": "s__Ferruginivarius sediminum", "ani": 78.6563, "matched_fragments": 409, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Ferruginivarius", "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_900100655.1", "gtdb_species": "s__Limimonas halophila", "ani": 78.5597, "matched_fragments": 318, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Limimonas", "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_006969625.1", "gtdb_species": "s__Algihabitans sp006969625", "ani": 78.0971, "matched_fragments": 366, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans", "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_007127165.1", "gtdb_species": "s__SKZV01 sp007127165", "ani": 77.6084, "matched_fragments": 234, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__SKZV01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.42", "min_intra_species_ani": "99.10", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900177295.1", "gtdb_species": "s__Tistlia consotensis", "ani": 77.5653, "matched_fragments": 438, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009377535.1", "gtdb_species": "s__WHTV01 sp009377535", "ani": 77.4958, "matched_fragments": 277, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01", "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_014925385.1", "gtdb_species": "s__WHTV01 sp014925385", "ani": 77.3933, "matched_fragments": 327, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01", "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_016699855.1", "gtdb_species": "s__GCA-016699855 sp016699855", "ani": 76.7463, "matched_fragments": 235, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855", "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_002924445.1", "gtdb_species": "s__Minwuia thermotolerans", "ani": 76.7014, "matched_fragments": 209, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.67", "min_intra_species_ani": "95.35", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016869915.1", "gtdb_species": "s__CAIOSQ01 sp016869915", "ani": 76.5584, "matched_fragments": 178, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.75", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014197915.1", "gtdb_species": "s__Rhodospira visakhapatnamensis", "ani": 76.5445, "matched_fragments": 205, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira", "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": -0.061, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 4176424.0, "gc_content": 66.0, "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": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Rhodovibrio", "salinarum", "DSM", "9154" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }