{ "type": "genome", "identifier": "GCA_026461575.1", "organism": "Rhodoferax sp.", "title": "Rhodoferax sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "University of Alberta", "publication": [ {} ], "properties": { "assembly_accession": "GCA_026461575.1", "bioproject": "PRJNA526747", "biosample": "SAMN27925767", "wgs_master": "JAPJMS000000000.1", "refseq_category": "na", "taxid": "50421", "species_taxid": "50421", "organism_name": "Rhodoferax sp.", "infraspecific_name": "", "isolate": "MAG07", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/28", "asm_name": "ASM2646157v1", "submitter": "University of Alberta", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/461/575/GCA_026461575.1_ASM2646157v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-11-28", "dateModified": "2022-11-28", "datePublished": "2022-11-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodoferax sp." ], "sample_taxid": [ "50421" ], "sample_host_organism": [ "Ephydatia muelleri" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada:Sooke River" ], "sample_host_location_id": [], "data_size": "0.651 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 75.0, "contamination": 0.46, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2284005", "Number of Sequences": "865", "Longest Sequences (bp)": "21092", "N50 (bp)": "3397", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.4", "Number of CDSs": "1363", "Average Protein Length": "281.2", "Coding Ratio (%)": "50.3", "Number of rRNAs": "0", "Number of tRNAs": "31", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodoferax lacus", "strain": "strain=IMCC26218", "accession": "GCA_003415675.1", "taxid": 2184758, "species_taxid": 2184758, "relation_to_type": "type", "validated": true, "ani": 79.2121, "matched_fragments": 130, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax saidenbachensis", "strain": "strain=DSM 22694", "accession": "GCA_001955715.1", "taxid": 1484693, "species_taxid": 1484693, "relation_to_type": "type", "validated": true, "ani": 78.2448, "matched_fragments": 92, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax saidenbachensis", "strain": "strain=ED16", "accession": "GCA_000498435.1", "taxid": 1484693, "species_taxid": 1484693, "relation_to_type": "type", "validated": true, "ani": 78.2175, "matched_fragments": 92, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax bucti", "strain": "strain=GSA243-2", "accession": "GCA_005876985.1", "taxid": 2576305, "species_taxid": 2576305, "relation_to_type": "type", "validated": true, "ani": 77.9785, "matched_fragments": 85, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax carolinensis", "strain": "strain=NA3", "accession": "GCA_002157145.1", "taxid": 553814, "species_taxid": 553814, "relation_to_type": "type", "validated": true, "ani": 77.1547, "matched_fragments": 79, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curvibacter lanceolatus", "strain": "strain=ATCC 14669", "accession": "GCA_000381265.1", "taxid": 86182, "species_taxid": 86182, "relation_to_type": "type", "validated": true, "ani": 77.1319, "matched_fragments": 71, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax soli", "strain": "strain=DSM 25157", "accession": "GCA_900107605.1", "taxid": 592050, "species_taxid": 592050, "relation_to_type": "type", "validated": true, "ani": 77.0787, "matched_fragments": 74, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga pseudoflava", "strain": "strain=NBRC 102511", "accession": "GCA_001592285.1", "taxid": 47421, "species_taxid": 47421, "relation_to_type": "type", "validated": true, "ani": 77.0173, "matched_fragments": 60, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax antarcticus", "strain": "strain=ANT.BR", "accession": "GCA_001938565.1", "taxid": 81479, "species_taxid": 81479, "relation_to_type": "type", "validated": true, "ani": 77.0134, "matched_fragments": 79, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ottowia beijingensis", "strain": "strain=GCS-AN-3", "accession": "GCA_013423955.1", "taxid": 1207057, "species_taxid": 1207057, "relation_to_type": "type", "validated": true, "ani": 77.009, "matched_fragments": 72, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax temperans", "strain": "strain=DSM 7270", "accession": "GCA_006716905.1", "taxid": 80878, "species_taxid": 80878, "relation_to_type": "type", "validated": true, "ani": 77.0054, "matched_fragments": 74, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax antarcticus", "strain": "strain=DSM 24876", "accession": "GCA_001955735.1", "taxid": 81479, "species_taxid": 81479, "relation_to_type": "type", "validated": true, "ani": 76.9961, "matched_fragments": 79, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax beijingensis", "strain": "strain=502", "accession": "GCA_003951285.1", "taxid": 2496117, "species_taxid": 2496117, "relation_to_type": "type", "validated": true, "ani": 76.9809, "matched_fragments": 60, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachymonas denitrificans", "strain": "strain=DSM 15123", "accession": "GCA_900110225.1", "taxid": 28220, "species_taxid": 28220, "relation_to_type": "type", "validated": true, "ani": 76.4243, "matched_fragments": 55, "total_fragments": 328, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 75.0, "contamination": 0.46, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_003415675.1", "gtdb_species": "s__Rhodoferax sp003415675", "ani": 79.2121, "matched_fragments": 130, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "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_903845935.1", "gtdb_species": "s__Rhodoferax sp903845935", "ani": 79.1453, "matched_fragments": 127, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.58", "min_intra_species_ani": "99.41", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCA_903886275.1", "gtdb_species": "s__Rhodoferax sp903886275", "ani": 78.6338, "matched_fragments": 131, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_001795455.1", "gtdb_species": "s__Rhodoferax sp001795455", "ani": 78.2934, "matched_fragments": 97, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001955715.1", "gtdb_species": "s__Rhodoferax saidenbachensis", "ani": 78.2448, "matched_fragments": 92, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "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": "GCA_903863395.1", "gtdb_species": "s__Rhodoferax sp903863395", "ani": 77.8733, "matched_fragments": 78, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.94", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.81", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_903870955.1", "gtdb_species": "s__Rhodoferax sp903870955", "ani": 77.8534, "matched_fragments": 67, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "98.51", "mean_intra_species_af": "0.73", "min_intra_species_af": "0.73", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002943465.1", "gtdb_species": "s__Rhodoferax sp002943465", "ani": 77.8399, "matched_fragments": 100, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "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_903897925.1", "gtdb_species": "s__Rhodoferax sp903897925", "ani": 77.726, "matched_fragments": 95, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.65", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016719405.1", "gtdb_species": "s__Rhodoferax sp016719405", "ani": 77.5896, "matched_fragments": 68, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006716905.1", "gtdb_species": "s__Acidovorax temperans", "ani": 77.0054, "matched_fragments": 74, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.32", "min_intra_species_ani": "95.61", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_011391545.1", "gtdb_species": "s__Rhodoferax sp011391545", "ani": 77.005, "matched_fragments": 57, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "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_900110225.1", "gtdb_species": "s__Brachymonas denitrificans", "ani": 76.4243, "matched_fragments": 55, "total_fragments": 328, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Brachymonas", "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": -0.359, "cell_length": 0.232, "doubling_h": 1.328, "growth_tmp": 24.158, "optimum_tmp": 20.583, "optimum_ph": null, "genome_size": 4428306.622, "gc_content": 59.232, "coding_genes": 4022.388, "rRNA16S_genes": 2.333, "tRNA_genes": 46.333, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.666, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.333, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "bacillus_cell_shape": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.333, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Rhodoferax_C", "s__" ], "_genome_taxon": [ "Rhodoferax", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Rhodoferax_C", "s__", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Burkholderiaceae", "Rhodoferax", "C", "s", "", "" ], "_meo": [ { "id": "MEO_0002677", "label": "sponge" }, { "id": "MEO_0000038", "label": "freshwater" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }