{ "type": "genome", "identifier": "GCA_021299035.1", "organism": "Oxalobacteraceae bacterium", "title": "Oxalobacteraceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of Michigan", "publication": [ {} ], "properties": { "assembly_accession": "GCA_021299035.1", "bioproject": "PRJNA464361", "biosample": "SAMN23604936", "wgs_master": "JAJTGD000000000.1", "refseq_category": "na", "taxid": "1871070", "species_taxid": "1871070", "organism_name": "Oxalobacteraceae bacterium", "infraspecific_name": "", "isolate": "49613_E42", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/12/27", "asm_name": "ASM2129903v1", "submitter": "University of Michigan", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/021/299/035/GCA_021299035.1_ASM2129903v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-12-27", "dateModified": "2021-12-27", "datePublished": "2021-12-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Oxalobacteraceae bacterium" ], "sample_taxid": [ "1871070" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Ohio, western Lake Erie, NOAA Station WE12" ], "sample_host_location_id": [], "data_size": "0.739 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2577464", "Number of Sequences": "80", "Longest Sequences (bp)": "151719", "N50 (bp)": "67793", "Gap Ratio (%)": "0.003686", "GCcontent (%)": "55.1", "Number of CDSs": "2411", "Average Protein Length": "308.2", "Coding Ratio (%)": "86.5", "Number of rRNAs": "1", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Noviherbaspirillum aridicola", "strain": "strain=NCCP-691", "accession": "GCA_019656455.1", "taxid": 2849687, "species_taxid": 2849687, "relation_to_type": "type", "validated": true, "ani": 76.8922, "matched_fragments": 115, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oxalicibacterium solurbis", "strain": "strain=CCM 7664", "accession": "GCA_014635845.1", "taxid": 69280, "species_taxid": 69280, "relation_to_type": "type", "validated": true, "ani": 76.8215, "matched_fragments": 117, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oxalicibacterium flavum", "strain": "strain=CCM 7086", "accession": "GCA_014635065.1", "taxid": 179467, "species_taxid": 179467, "relation_to_type": "type", "validated": true, "ani": 76.818, "matched_fragments": 108, "total_fragments": 819, "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": 76.8167, "matched_fragments": 113, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum hiltneri", "strain": "strain=N3", "accession": "GCA_001267925.1", "taxid": 341045, "species_taxid": 341045, "relation_to_type": "type", "validated": true, "ani": 76.7744, "matched_fragments": 106, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum rubrisubalbicans", "strain": "strain=DSM 11543", "accession": "GCA_003719195.1", "taxid": 80842, "species_taxid": 80842, "relation_to_type": "type", "validated": true, "ani": 76.7266, "matched_fragments": 97, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum rubrisubalbicans", "strain": "strain=NBRC 102523", "accession": "GCA_001591225.1", "taxid": 80842, "species_taxid": 80842, "relation_to_type": "type", "validated": true, "ani": 76.7197, "matched_fragments": 94, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas arenae", "strain": "strain=Ter10", "accession": "GCA_001584165.1", "taxid": 279058, "species_taxid": 279058, "relation_to_type": "type", "validated": true, "ani": 76.712, "matched_fragments": 95, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas pratensis", "strain": "strain=Ter91", "accession": "GCA_001584185.1", "taxid": 279113, "species_taxid": 279113, "relation_to_type": "type", "validated": true, "ani": 76.693, "matched_fragments": 97, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum humi", "strain": "strain=U15", "accession": "GCA_900188095.1", "taxid": 1688639, "species_taxid": 1688639, "relation_to_type": "type", "validated": true, "ani": 76.6814, "matched_fragments": 106, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum pedocola", "strain": "strain=DKR-6", "accession": "GCA_016632335.1", "taxid": 2801341, "species_taxid": 2801341, "relation_to_type": "type", "validated": true, "ani": 76.6578, "matched_fragments": 145, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia agilis", "strain": "strain=JCM 31605", "accession": "GCA_024756255.1", "taxid": 1811226, "species_taxid": 1811226, "relation_to_type": "type", "validated": true, "ani": 76.6232, "matched_fragments": 91, "total_fragments": 819, "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": 76.5296, "matched_fragments": 101, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum galbum", "strain": "strain=17J57-3", "accession": "GCA_010974945.1", "taxid": 2709383, "species_taxid": 2709383, "relation_to_type": "type", "validated": true, "ani": 76.5244, "matched_fragments": 107, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia soli", "strain": "strain=R798", "accession": "GCA_016809835.2", "taxid": 2792854, "species_taxid": 2792854, "relation_to_type": "type", "validated": true, "ani": 76.4948, "matched_fragments": 95, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella dendranthematis", "strain": "strain=AF9R3", "accession": "GCA_012849375.1", "taxid": 2728021, "species_taxid": 2728021, "relation_to_type": "type", "validated": true, "ani": 76.4849, "matched_fragments": 100, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia niastensis", "strain": "strain=DSM 21313", "accession": "GCA_000382345.1", "taxid": 544911, "species_taxid": 544911, "relation_to_type": "type", "validated": true, "ani": 76.4472, "matched_fragments": 93, "total_fragments": 819, "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": 76.4454, "matched_fragments": 82, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella aceris", "strain": "strain=SAP-35", "accession": "GCA_011090165.1", "taxid": 2703883, "species_taxid": 2703883, "relation_to_type": "type", "validated": true, "ani": 76.3893, "matched_fragments": 96, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella lutea", "strain": "strain=DSM 17473", "accession": "GCA_004209755.1", "taxid": 321985, "species_taxid": 321985, "relation_to_type": "type", "validated": true, "ani": 76.3859, "matched_fragments": 77, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia terrae", "strain": "strain=JCM 31606", "accession": "GCA_024753145.1", "taxid": 1811224, "species_taxid": 1811224, "relation_to_type": "type", "validated": true, "ani": 76.3698, "matched_fragments": 107, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella umbonata", "strain": "strain=CECT 7753", "accession": "GCA_014192225.1", "taxid": 864828, "species_taxid": 864828, "relation_to_type": "type", "validated": true, "ani": 76.3602, "matched_fragments": 89, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella lactea", "strain": "strain=FT50W", "accession": "GCA_009857505.1", "taxid": 2692173, "species_taxid": 2692173, "relation_to_type": "type", "validated": true, "ani": 76.3073, "matched_fragments": 81, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella alba", "strain": "strain=FT9W", "accession": "GCA_009674495.1", "taxid": 2666081, "species_taxid": 2666081, "relation_to_type": "type", "validated": true, "ani": 76.298, "matched_fragments": 98, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella callida", "strain": "strain=DN04", "accession": "GCA_004614165.1", "taxid": 2561932, "species_taxid": 2561932, "relation_to_type": "type", "validated": true, "ani": 76.2246, "matched_fragments": 102, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella sacchari", "strain": "strain=Sac-22", "accession": "GCA_900143065.1", "taxid": 551987, "species_taxid": 551987, "relation_to_type": "type", "validated": true, "ani": 76.1387, "matched_fragments": 99, "total_fragments": 819, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_018882935.1", "gtdb_species": "s__SYFN01 sp018882935", "ani": 80.7575, "matched_fragments": 480, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.35", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016868055.1", "gtdb_species": "s__SYFN01 sp016868055", "ani": 80.6983, "matched_fragments": 451, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01", "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_010024875.1", "gtdb_species": "s__SYFN01 sp010024875", "ani": 77.2409, "matched_fragments": 197, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01", "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_004342585.1", "gtdb_species": "s__Paucimonas lemoignei", "ani": 77.0791, "matched_fragments": 95, "total_fragments": 819, "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": "GCA_016467405.1", "gtdb_species": "s__Lacisediminimonas sp016467405", "ani": 76.9753, "matched_fragments": 108, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas", "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_900299005.1", "gtdb_species": "s__SYFN01 sp900299005", "ani": 76.9741, "matched_fragments": 154, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004114795.1", "gtdb_species": "s__Paucimonas sp004114795", "ani": 76.9513, "matched_fragments": 91, "total_fragments": 819, "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_000577615.1", "gtdb_species": "s__Herbaspirillum sp000577615", "ani": 76.8631, "matched_fragments": 102, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_014635065.1", "gtdb_species": "s__Oxalicibacterium flavum", "ani": 76.8385, "matched_fragments": 107, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium", "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_000282135.1", "gtdb_species": "s__Herbaspirillum sp000282135", "ani": 76.794, "matched_fragments": 95, "total_fragments": 819, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_004570315.1", "gtdb_species": "s__Noviherbaspirillum sp004570315", "ani": 76.7703, "matched_fragments": 100, "total_fragments": 819, "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": "-" }, { "accession": "GCF_003590835.1", "gtdb_species": "s__Paucimonas 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