{ "type": "genome", "identifier": "GCA_027484865.1", "organism": "Rhodobacter sp.", "title": "Rhodobacter sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Montreal", "publication": [ {} ], "properties": { "assembly_accession": "GCA_027484865.1", "bioproject": "PRJNA767443", "biosample": "SAMN21888850", "wgs_master": "JAIXSC000000000.1", "refseq_category": "na", "taxid": "1062", "species_taxid": "1062", "organism_name": "Rhodobacter sp.", "infraspecific_name": "", "isolate": "C4_MAG_00087", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/12/28", "asm_name": "ASM2748486v1", "submitter": "University of Montreal", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/027/484/865/GCA_027484865.1_ASM2748486v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-12-28", "dateModified": "2022-12-28", "datePublished": "2022-12-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodobacter sp." ], "sample_taxid": [ "1062" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Gault Nature Reserve" ], "sample_host_location_id": [], "data_size": "1.138 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 76.33, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4107736", "Number of Sequences": "96", "Longest Sequences (bp)": "247532", "N50 (bp)": "72446", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.9", "Number of CDSs": "3975", "Average Protein Length": "302.7", "Coding Ratio (%)": "87.9", "Number of rRNAs": "0", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gemmobacter aquarius", "strain": "strain=HYN0069", "accession": "GCA_003060865.1", "taxid": 2169400, "species_taxid": 2169400, "relation_to_type": "type", "validated": true, "ani": 98.8558, "matched_fragments": 1192, "total_fragments": 1319, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gemmobacter straminiformis", "strain": "strain=CAM-8", "accession": "GCA_014243445.1", "taxid": 2045119, "species_taxid": 2045119, "relation_to_type": "type", "validated": true, "ani": 84.2584, "matched_fragments": 885, "total_fragments": 1319, "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": 81.4749, "matched_fragments": 741, "total_fragments": 1319, "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": 81.45, "matched_fragments": 744, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter ruber", "strain": "strain=CCP-1", "accession": "GCA_009908315.1", "taxid": 1985673, "species_taxid": 1985673, "relation_to_type": "type", "validated": true, "ani": 80.3078, "matched_fragments": 698, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola algicola", "strain": "strain=ETT8", "accession": "GCA_010915705.1", "taxid": 2709381, "species_taxid": 2709381, "relation_to_type": "type", "validated": true, "ani": 79.8491, "matched_fragments": 557, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 79.2623, "matched_fragments": 522, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tabrizicola alkalilacus", "strain": "strain=DJC", "accession": "GCA_003443995.1", "taxid": 2305252, "species_taxid": 2305252, "relation_to_type": "type", "validated": true, "ani": 79.0063, "matched_fragments": 506, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter caeruleus", "strain": "strain=N8", "accession": "GCA_008271655.1", "taxid": 2595004, "species_taxid": 2595004, "relation_to_type": "type", "validated": true, "ani": 78.9096, "matched_fragments": 544, "total_fragments": 1319, "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": 78.8307, "matched_fragments": 509, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter nectariphilus", "strain": "strain=DSM 15620", "accession": "GCA_000429765.1", "taxid": 220343, "species_taxid": 220343, "relation_to_type": "type", "validated": true, "ani": 78.797, "matched_fragments": 431, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter lanyuensis", "strain": "strain=KCTC 23714", "accession": "GCA_014652355.1", "taxid": 1054497, "species_taxid": 1054497, "relation_to_type": "type", "validated": true, "ani": 78.7616, "matched_fragments": 475, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 78.7348, "matched_fragments": 537, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter changlensis", "strain": "strain=DSM 18774", "accession": "GCA_003254335.1", "taxid": 402884, "species_taxid": 402884, "relation_to_type": "type", "validated": true, "ani": 78.715, "matched_fragments": 511, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter megaterium", "strain": "strain=DSM 26375", "accession": "GCA_900156815.1", "taxid": 1086013, "species_taxid": 1086013, "relation_to_type": "type", "validated": true, "ani": 77.954, "matched_fragments": 311, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 77.9495, "matched_fragments": 411, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter megaterium", "strain": "strain=CGMCC 1.11024", "accession": "GCA_014636395.1", "taxid": 1086013, "species_taxid": 1086013, "relation_to_type": "type", "validated": true, "ani": 77.9345, "matched_fragments": 313, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter azotoformans", "strain": "strain=KA25", "accession": "GCA_003050905.1", "taxid": 43057, "species_taxid": 43057, "relation_to_type": "type", "validated": true, "ani": 77.9256, "matched_fragments": 410, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cypionkella psychrotolerans", "strain": "strain=PAMC 27389", "accession": "GCA_001294535.1", "taxid": 1678131, "species_taxid": 1678131, "relation_to_type": "type", "validated": true, "ani": 77.6563, "matched_fragments": 398, "total_fragments": 1319, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 76.33, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_003060865.1", "gtdb_species": "s__Gemmobacter_B sp003060865", "ani": 98.8558, "matched_fragments": 1192, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_014243445.1", "gtdb_species": "s__Gemmobacter_B straminiformis", "ani": 84.2668, "matched_fragments": 884, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_009908265.2", "gtdb_species": "s__Gemmobacter_B sp009908265", "ani": 81.481, "matched_fragments": 741, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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": "-" }, { "accession": "GCF_011059185.1", "gtdb_species": "s__Gemmobacter_B sp011059185", "ani": 80.5496, "matched_fragments": 724, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_000500915.1", "gtdb_species": "s__Gemmobacter_B sp000500915", "ani": 80.4455, "matched_fragments": 603, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_002256185.1", "gtdb_species": "s__Gemmobacter_B sp002256185", "ani": 79.8159, "matched_fragments": 594, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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_001828855.1", "gtdb_species": "s__Cypionkella sp001828855", "ani": 79.7127, "matched_fragments": 597, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900110025.1", "gtdb_species": "s__Gemmobacter aquatilis", "ani": 79.2628, "matched_fragments": 522, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_014859945.1", "gtdb_species": "s__UBA1943 sp014859945", "ani": 79.2372, "matched_fragments": 445, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943", "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_003443995.1", "gtdb_species": "s__ETT8 sp003443995", "ani": 79.007, "matched_fragments": 506, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8", "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_015999335.1", "gtdb_species": "s__Tabrizicola soli", "ani": 78.9213, "matched_fragments": 533, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola", "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_008271655.1", "gtdb_species": "s__Gemmobacter caeruleus", "ani": 78.9008, "matched_fragments": 546, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter", "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_011008935.1", "gtdb_species": "s__KMS-5 sp011008935", "ani": 78.8759, "matched_fragments": 532, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5", "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_000429765.1", "gtdb_species": "s__Wagnerdoeblera nectariphila", "ani": 78.7582, "matched_fragments": 435, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera", "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_016765775.1", "gtdb_species": "s__Pseudorhodobacter sp016765775", "ani": 78.5601, "matched_fragments": 413, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter", "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_003053725.1", "gtdb_species": "s__Rhodovulum kholense", "ani": 77.4492, "matched_fragments": 328, "total_fragments": 1319, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.102, "cell_length": 0.166, "doubling_h": 0.531, "growth_tmp": 28.333, "optimum_tmp": 30.312, "optimum_ph": 6.9, "genome_size": 4127409.974, "gc_content": 66.914, "coding_genes": 3782.589, "rRNA16S_genes": 3.9, "tRNA_genes": 50.925, "gram_stain": 0.0, "sporulation": 0.2, "motility": 0.625, "range_salinity": 0.0, "facultative_respiration": 0.333, "anaerobic_respiration": 0.333, "aerobic_respiration": 0.333, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.5, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.5, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodobacterales", "f__Rhodobacteraceae", "g__Gemmobacter_B", "s__Gemmobacter_B aquarius" ], "_genome_taxon": [ "Rhodobacter", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhodobacterales", "f__Rhodobacteraceae", "g__Gemmobacter_B", "s__Gemmobacter_B aquarius", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhodobacterales", "Rhodobacteraceae", "Gemmobacter", "B", "Gemmobacter", "B", "aquarius" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000027", "label": "pond" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }