{ "type": "genome", "identifier": "GCA_020048475.1", "organism": "Rhodoferax sp.", "title": "Rhodoferax sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Michigan", "publication": [ {} ], "properties": { "assembly_accession": "GCA_020048475.1", "bioproject": "PRJNA72255", "biosample": "SAMN20441962", "wgs_master": "JAIFMM000000000.1", "refseq_category": "na", "taxid": "50421", "species_taxid": "50421", "organism_name": "Rhodoferax sp.", "infraspecific_name": "", "isolate": "bin_38", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/09/20", "asm_name": "ASM2004847v1", "submitter": "University of Michigan", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/048/475/GCA_020048475.1_ASM2004847v1", "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": "2021-09-20", "dateModified": "2021-09-20", "datePublished": "2021-09-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodoferax sp." ], "sample_taxid": [ "50421" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: northwestern Lake Huron" ], "sample_host_location_id": [], "data_size": "0.337 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 12.5, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1189669", "Number of Sequences": "145", "Longest Sequences (bp)": "21853", "N50 (bp)": "8257", "Gap Ratio (%)": "0.001681", "GCcontent (%)": "58.2", "Number of CDSs": "964", "Average Protein Length": "316.6", "Coding Ratio (%)": "77.0", "Number of rRNAs": "0", "Number of tRNAs": "9", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodoferax fermentans", "strain": "strain=JCM 7819", "accession": "GCA_002017865.1", "taxid": 28066, "species_taxid": 28066, "relation_to_type": "type", "validated": true, "ani": 78.6645, "matched_fragments": 120, "total_fragments": 327, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax fermentans", "strain": "strain=DSM 10138", "accession": "GCA_016583655.1", "taxid": 28066, "species_taxid": 28066, "relation_to_type": "type", "validated": true, "ani": 78.6257, "matched_fragments": 120, "total_fragments": 327, "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": 77.9817, "matched_fragments": 110, "total_fragments": 327, "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": 77.9678, "matched_fragments": 108, "total_fragments": 327, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoferax lacus", "strain": "strain=IMCC26218", "accession": "GCA_003415675.1", "taxid": 2184758, "species_taxid": 2184758, "relation_to_type": "type", "validated": true, "ani": 77.3186, "matched_fragments": 77, "total_fragments": 327, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 12.5, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_016719055.1", "gtdb_species": "s__Rhodoferax sp016719055", "ani": 91.475, "matched_fragments": 278, "total_fragments": 327, "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_903873485.1", "gtdb_species": "s__Rhodoferax sp903873485", "ani": 79.6059, "matched_fragments": 171, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.21", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_002083775.1", "gtdb_species": "s__Rhodoferax ferrireducens_A", "ani": 78.8263, "matched_fragments": 134, "total_fragments": 327, "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_002784245.1", "gtdb_species": "s__Rhodoferax sp002784245", "ani": 77.8752, "matched_fragments": 66, "total_fragments": 327, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003415675.1", "gtdb_species": "s__Rhodoferax sp003415675", "ani": 77.3186, "matched_fragments": 77, "total_fragments": 327, "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": "-" } ] }, "_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", "s__" ], "_genome_taxon": [ "Rhodoferax", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Rhodoferax", "s__", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Burkholderiaceae", "Rhodoferax", "s", "", "" ], "_meo": [ { "id": "MEO_0000116", "label": "biofilm" }, { "id": "MEO_0000038", "label": "freshwater" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }