{ "type": "genome", "identifier": "GCA_903900865.1", "organism": "uncultured beta proteobacterium", "title": "uncultured beta proteobacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "BILS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_903900865.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6954336", "wgs_master": "CAIUOW000000000.1", "refseq_category": "na", "taxid": "86027", "species_taxid": "86027", "organism_name": "uncultured beta proteobacterium", "infraspecific_name": "", "isolate": "KTt_bin-0542", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/19", "asm_name": "freshwater MAG --- KTt_bin-0542", "submitter": "BILS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/900/865/GCA_903900865.1_freshwater_MAG_---_KTt_bin-0542", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-19", "dateModified": "2020-07-19", "datePublished": "2020-07-19", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured beta proteobacterium" ], "sample_taxid": [ "86027" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Sweden" ], "sample_host_location_id": [], "data_size": "0.972 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 49.31, "contamination": 2.08, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3429322", "Number of Sequences": "238", "Longest Sequences (bp)": "125511", "N50 (bp)": "33625", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.1", "Number of CDSs": "2939", "Average Protein Length": "328.8", "Coding Ratio (%)": "84.5", "Number of rRNAs": "1", "Number of tRNAs": "22", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodoferax ferrireducens", "strain": "strain=DSM 15236", "accession": "GCA_000013605.1", "taxid": 192843, "species_taxid": 192843, "relation_to_type": "type", "validated": true, "ani": 79.1828, "matched_fragments": 422, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter tataouinensis", "strain": "strain=TTB310", "accession": "GCA_000215705.1", "taxid": 94132, "species_taxid": 94132, "relation_to_type": "type", "validated": true, "ani": 77.7448, "matched_fragments": 263, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax paradoxus", "strain": "strain=NBRC 15149", "accession": "GCA_001591365.1", "taxid": 34073, "species_taxid": 34073, "relation_to_type": "suspected-type", "validated": true, "ani": 77.5674, "matched_fragments": 273, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Limnohabitans radicicola", "strain": "strain=JUR4", "accession": "GCA_014837235.1", "taxid": 2771427, "species_taxid": 2771427, "relation_to_type": "type", "validated": true, "ani": 77.5461, "matched_fragments": 194, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter pinisoli", "strain": "strain=MAH-25", "accession": "GCA_009758015.1", "taxid": 2682844, "species_taxid": 2682844, "relation_to_type": "type", "validated": true, "ani": 77.4646, "matched_fragments": 254, "total_fragments": 1017, "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": 77.4215, "matched_fragments": 270, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variovorax guangxiensis", "strain": "strain=DSM 27352", "accession": "GCA_003952165.1", "taxid": 1775474, "species_taxid": 1775474, "relation_to_type": "type", "validated": true, "ani": 77.1123, "matched_fragments": 248, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax aquaticus", "strain": "strain=Gr-4", "accession": "GCA_006974105.1", "taxid": 2527691, "species_taxid": 2527691, "relation_to_type": "type", "validated": true, "ani": 77.0133, "matched_fragments": 147, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Diaphorobacter caeni", "strain": "strain=NR2-3-3-1", "accession": "GCA_015354245.1", "taxid": 2784387, "species_taxid": 2784387, "relation_to_type": "type", "validated": true, "ani": 76.675, "matched_fragments": 190, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquabacterium soli", "strain": "strain=SJQ9", "accession": "GCA_003933735.1", "taxid": 2493092, "species_taxid": 2493092, "relation_to_type": "type", "validated": true, "ani": 76.5432, "matched_fragments": 150, "total_fragments": 1017, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 49.31, "contamination": 2.08, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_002413825.1", "gtdb_species": "s__Rhodoferax sp002413825", "ani": 80.322, "matched_fragments": 429, "total_fragments": 1017, "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_012927445.1", "gtdb_species": "s__Rhodoferax sp012927445", "ani": 79.7826, "matched_fragments": 387, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003347515.1", "gtdb_species": "s__Rhodoferax sp003347515", "ani": 79.7357, "matched_fragments": 475, "total_fragments": 1017, "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_002422455.1", "gtdb_species": "s__Rhodoferax sp002422455", "ani": 79.4252, "matched_fragments": 211, "total_fragments": 1017, "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_000013605.1", "gtdb_species": "s__Rhodoferax ferrireducens", "ani": 79.1964, "matched_fragments": 420, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.18", "min_intra_species_ani": "95.18", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_010365055.1", "gtdb_species": "s__Rhodoferax sp010365055", "ani": 78.8625, "matched_fragments": 378, "total_fragments": 1017, "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_018780565.1", "gtdb_species": "s__Rhodoferax sp018780565", "ani": 78.8507, "matched_fragments": 348, "total_fragments": 1017, "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_011391645.1", "gtdb_species": "s__Rhodoferax sp011391645", "ani": 78.5458, "matched_fragments": 226, "total_fragments": 1017, "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_013791765.1", "gtdb_species": "s__Rhodoferax sp013791765", "ani": 78.3754, "matched_fragments": 362, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.92", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_017880985.1", "gtdb_species": "s__Rhodoferax sp017880985", "ani": 78.3267, "matched_fragments": 241, "total_fragments": 1017, "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_000175235.1", "gtdb_species": "s__Acidovorax delafieldii_B", "ani": 77.4379, "matched_fragments": 205, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax", "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_018241405.1", "gtdb_species": "s__Alicycliphilus sp018241405", "ani": 77.371, "matched_fragments": 205, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018240985.1", "gtdb_species": "s__Alicycliphilus sp018240985", "ani": 77.24, "matched_fragments": 193, "total_fragments": 1017, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.65", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Rhodoferax", "s__" ], "_genome_taxon": [ "uncultured", "beta", "proteobacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Rhodoferax", "s__", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Burkholderiaceae", "Rhodoferax", "s", "", "" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }