{ "type": "genome", "identifier": "GCA_903862415.1", "organism": "uncultured Oxalobacteraceae bacterium", "title": "uncultured Oxalobacteraceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "BILS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_903862415.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6953718", "wgs_master": "CAIOYD000000000.1", "refseq_category": "na", "taxid": "253871", "species_taxid": "253871", "organism_name": "uncultured Oxalobacteraceae bacterium", "infraspecific_name": "", "isolate": "MJ-time_bin-6643", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/19", "asm_name": "freshwater MAG --- MJ-time_bin-6643", "submitter": "BILS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/862/415/GCA_903862415.1_freshwater_MAG_---_MJ-time_bin-6643", "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 Oxalobacteraceae bacterium" ], "sample_taxid": [ "253871" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Finland" ], "sample_host_location_id": [], "data_size": "1.023 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 66.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3584134", "Number of Sequences": "78", "Longest Sequences (bp)": "237738", "N50 (bp)": "92574", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.8", "Number of CDSs": "3098", "Average Protein Length": "344.1", "Coding Ratio (%)": "89.2", "Number of rRNAs": "0", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sapientia aquatica", "strain": "strain=SA-152", "accession": "GCA_004358105.1", "taxid": 1549640, "species_taxid": 1549640, "relation_to_type": "type", "validated": true, "ani": 78.2885, "matched_fragments": 301, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Solimicrobium silvestre", "strain": "strain=S20-91", "accession": "GCA_002976435.1", "taxid": 2099400, "species_taxid": 2099400, "relation_to_type": "type", "validated": true, "ani": 78.1578, "matched_fragments": 335, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium aquatile", "strain": "strain=CCTCC AB 2015119", "accession": "GCA_014699135.1", "taxid": 1537398, "species_taxid": 1537398, "relation_to_type": "type", "validated": true, "ani": 76.917, "matched_fragments": 135, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium hunanense", "strain": "strain=CY18W", "accession": "GCA_014284335.1", "taxid": 2762292, "species_taxid": 2762292, "relation_to_type": "type", "validated": true, "ani": 76.8647, "matched_fragments": 175, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium parvum", "strain": "strain=DSM 23061", "accession": "GCA_003955735.1", "taxid": 401471, "species_taxid": 401471, "relation_to_type": "type", "validated": true, "ani": 76.8209, "matched_fragments": 127, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium griseum", "strain": "strain=FT31W", "accession": "GCA_014284195.1", "taxid": 2762295, "species_taxid": 2762295, "relation_to_type": "type", "validated": true, "ani": 76.7153, "matched_fragments": 153, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas antrihumi", "strain": "strain=DSM 104040", "accession": "GCA_018304965.1", "taxid": 1940615, "species_taxid": 1940615, "relation_to_type": "type", "validated": true, "ani": 76.6949, "matched_fragments": 130, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum autotrophicum", "strain": "strain=IAM 14942", "accession": "GCA_001189915.1", "taxid": 180195, "species_taxid": 180195, "relation_to_type": "type", "validated": true, "ani": 76.6865, "matched_fragments": 146, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium umbellatum", "strain": "strain=NL8W", "accession": "GCA_014284125.1", "taxid": 2762300, "species_taxid": 2762300, "relation_to_type": "type", "validated": true, "ani": 76.6727, "matched_fragments": 143, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janthinobacterium tructae", "strain": "strain=SNU WT3", "accession": "GCA_006517255.1", "taxid": 2590869, "species_taxid": 2590869, "relation_to_type": "type", "validated": true, "ani": 76.6704, "matched_fragments": 115, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium amnicola", "strain": "strain=KCTC 52442", "accession": "GCA_014284275.1", "taxid": 1834038, "species_taxid": 1834038, "relation_to_type": "type", "validated": true, "ani": 76.6218, "matched_fragments": 96, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herminiimonas arsenitoxidans", "strain": "strain=AS8", "accession": "GCA_900130075.1", "taxid": 1809410, "species_taxid": 1809410, "relation_to_type": "type", "validated": true, "ani": 76.5451, "matched_fragments": 117, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas humicola", "strain": "strain=RLT1W51", "accession": "GCA_018304945.1", "taxid": 2825886, "species_taxid": 2825886, "relation_to_type": "type", "validated": true, "ani": 76.5308, "matched_fragments": 119, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium rugosum", "strain": "strain=CY7W", "accession": "GCA_014284365.1", "taxid": 2762291, "species_taxid": 2762291, "relation_to_type": "type", "validated": true, "ani": 76.508, "matched_fragments": 145, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Undibacterium oligocarboniphilum", "strain": "strain=EM 1", "accession": "GCA_013377855.1", "taxid": 666702, "species_taxid": 666702, "relation_to_type": "type", "validated": true, "ani": 76.4635, "matched_fragments": 157, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella aquatica", "strain": "strain=FT127W", "accession": "GCA_009857595.1", "taxid": 2660641, "species_taxid": 2660641, "relation_to_type": "type", "validated": true, "ani": 76.0472, "matched_fragments": 84, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rugamonas brunnea", "strain": "strain=LX20W", "accession": "GCA_014042345.1", "taxid": 2758569, "species_taxid": 2758569, "relation_to_type": "type", "validated": true, "ani": 76.0213, "matched_fragments": 83, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rugamonas fusca", "strain": "strain=FT3S", "accession": "GCA_014042365.1", "taxid": 2758568, "species_taxid": 2758568, "relation_to_type": "type", "validated": true, "ani": 75.9626, "matched_fragments": 85, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella guangdongensis", "strain": "strain=DS3", "accession": "GCA_009857475.1", "taxid": 2692179, "species_taxid": 2692179, "relation_to_type": "type", "validated": true, "ani": 75.9526, "matched_fragments": 76, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum cavernae", "strain": "strain=K2R10-39", "accession": "GCA_003590875.1", "taxid": 2320862, "species_taxid": 2320862, "relation_to_type": "type", "validated": true, "ani": 75.914, "matched_fragments": 81, "total_fragments": 1152, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 66.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903862415.1", "gtdb_species": "s__Solimicrobium sp903862415", "ani": 100.0, "matched_fragments": 1148, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_004358105.1", "gtdb_species": "s__Solimicrobium aquaticum", "ani": 78.2885, "matched_fragments": 301, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium", "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_002976435.1", "gtdb_species": "s__Solimicrobium silvestre", "ani": 78.1578, "matched_fragments": 335, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium", "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_903893945.1", "gtdb_species": "s__Solimicrobium sp903893945", "ani": 77.2722, "matched_fragments": 223, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.85", "min_intra_species_ani": "99.85", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014284335.1", "gtdb_species": "s__Undibacterium sp014284335", "ani": 76.879, "matched_fragments": 175, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_016200895.1", "gtdb_species": "s__Undibacterium sp016200895", "ani": 76.7795, "matched_fragments": 135, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_014284195.1", "gtdb_species": "s__Undibacterium sp014284195", "ani": 76.7305, "matched_fragments": 152, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_018304965.1", "gtdb_species": "s__Collimonas antrihumi", "ani": 76.6949, "matched_fragments": 130, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas", "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_002384815.1", "gtdb_species": "s__Herminiimonas sp002384815", "ani": 76.6675, "matched_fragments": 100, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas", "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_900130075.1", "gtdb_species": "s__Herminiimonas arsenitoxidans", "ani": 76.5621, "matched_fragments": 116, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas", "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_018304945.1", "gtdb_species": "s__Collimonas sp018304945", "ani": 76.5496, "matched_fragments": 119, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009857835.1", "gtdb_species": "s__Duganella fentianensis", "ani": 76.4904, "matched_fragments": 125, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella", "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_016196925.1", "gtdb_species": "s__Undibacterium sp016196925", "ani": 76.4744, "matched_fragments": 138, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium", "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_004114795.1", "gtdb_species": "s__Paucimonas sp004114795", "ani": 76.4639, "matched_fragments": 96, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas", "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_018305005.1", "gtdb_species": "s__Collimonas sp018305005", "ani": 76.3253, "matched_fragments": 128, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas", "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_007874125.1", "gtdb_species": "s__Noviherbaspirillum sp007874125", "ani": 76.0966, "matched_fragments": 82, "total_fragments": 1152, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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": -0.18, "cell_length": 0.222, "doubling_h": null, "growth_tmp": 27.559, "optimum_tmp": 27.563, "optimum_ph": 6.996, "genome_size": 5561458.093, "gc_content": 58.578, "coding_genes": 4230.172, "rRNA16S_genes": 3.192, "tRNA_genes": 58.705, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.883, "range_salinity": 0.0, "facultative_respiration": 0.015, "anaerobic_respiration": 0.015, "aerobic_respiration": 0.968, "mesophilic_range_tmp": 0.933, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.066, "bacillus_cell_shape": 0.921, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.019, "vibrio_cell_shape": 0.019, "spiral_cell_shape": 0.039 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Solimicrobium", "s__Solimicrobium sp903862415" ], "_genome_taxon": [ "uncultured", "Oxalobacteraceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Solimicrobium", "s__Solimicrobium sp903862415", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Burkholderiaceae", "Solimicrobium", "Solimicrobium", "sp903862415" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }