{ "type": "genome", "identifier": "GCA_026400425.1", "organism": "Hyphomicrobiales bacterium", "title": "Hyphomicrobiales bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Jill Banfield's Lab at Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_026400425.1", "bioproject": "PRJNA852163", "biosample": "SAMN30026363", "wgs_master": "JAPLPC000000000.1", "refseq_category": "na", "taxid": "1909294", "species_taxid": "1909294", "organism_name": "Hyphomicrobiales bacterium", "infraspecific_name": "", "isolate": "LacPavin_0419_WC53_MAG_62_6", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/24", "asm_name": "ASM2640042v1", "submitter": "Jill Banfield's Lab at Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/400/425/GCA_026400425.1_ASM2640042v1", "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": "2022-11-24", "dateModified": "2022-11-24", "datePublished": "2022-11-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Hyphomicrobiales bacterium" ], "sample_taxid": [ "1909294" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Besse-et-Saint-Anastaise, Lac Pavin" ], "sample_host_location_id": [], "data_size": "1.379 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 76.84, "contamination": 4.69, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4911291", "Number of Sequences": "677", "Longest Sequences (bp)": "43029", "N50 (bp)": "9795", "Gap Ratio (%)": "0.134221", "GCcontent (%)": "62.4", "Number of CDSs": "4342", "Average Protein Length": "273.2", "Coding Ratio (%)": "72.5", "Number of rRNAs": "1", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodopseudomonas rhenobacensis", "strain": "strain=DSM 12706", "accession": "GCA_014203125.1", "taxid": 87461, "species_taxid": 87461, "relation_to_type": "type", "validated": true, "ani": 79.8551, "matched_fragments": 559, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium oropedii", "strain": "strain=Pear76", "accession": "GCA_020889685.1", "taxid": 1571201, "species_taxid": 1571201, "relation_to_type": "type", "validated": true, "ani": 79.6976, "matched_fragments": 621, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopseudomonas pentothenatexigens", "strain": "strain=JA575", "accession": "GCA_900218015.1", "taxid": 999699, "species_taxid": 999699, "relation_to_type": "type", "validated": true, "ani": 79.5857, "matched_fragments": 581, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopseudomonas pentothenatexigens", "strain": "strain=JA575", "accession": "GCA_003385925.1", "taxid": 999699, "species_taxid": 999699, "relation_to_type": "type", "validated": true, "ani": 79.5795, "matched_fragments": 583, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium sediminis", "strain": "strain=S2-20-1", "accession": "GCA_018736085.1", "taxid": 2840469, "species_taxid": 2840469, "relation_to_type": "type", "validated": true, "ani": 79.5735, "matched_fragments": 589, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium embrapense", "strain": "strain=SEMIA 6208", "accession": "GCA_001189235.2", "taxid": 630921, "species_taxid": 630921, "relation_to_type": "type", "validated": true, "ani": 79.5725, "matched_fragments": 650, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium amphicarpaeae", "strain": "strain=39S1MB", "accession": "GCA_002266435.2", "taxid": 1404768, "species_taxid": 1404768, "relation_to_type": "type", "validated": true, "ani": 79.5648, "matched_fragments": 636, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium nitroreducens", "strain": "strain=TSA1", "accession": "GCA_002776695.1", "taxid": 709803, "species_taxid": 709803, "relation_to_type": "type", "validated": true, "ani": 79.5496, "matched_fragments": 660, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium lablabi", "strain": "strain=CCBAU 23086", "accession": "GCA_001440475.1", "taxid": 722472, "species_taxid": 722472, "relation_to_type": "suspected-type", "validated": true, "ani": 79.5417, "matched_fragments": 636, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopseudomonas pseudopalustris", "strain": "strain=DSM 123", "accession": "GCA_900110435.1", "taxid": 1513892, "species_taxid": 1513892, "relation_to_type": "type", "validated": true, "ani": 79.5348, "matched_fragments": 580, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=USDA 76", "accession": "GCA_023278185.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 79.5153, "matched_fragments": 681, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=NBRC 14791", "accession": "GCA_006539665.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 79.5073, "matched_fragments": 667, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium elkanii", "strain": "strain=USDA 76", "accession": "GCA_000379145.1", "taxid": 29448, "species_taxid": 29448, "relation_to_type": "type", "validated": true, "ani": 79.5026, "matched_fragments": 692, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium frederickii", "strain": "strain=CNPSo 3426", "accession": "GCA_004570865.1", "taxid": 2560054, "species_taxid": 2560054, "relation_to_type": "type", "validated": true, "ani": 79.488, "matched_fragments": 614, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium paxllaeri", "strain": "strain=LMTR 21", "accession": "GCA_001693515.2", "taxid": 190148, "species_taxid": 190148, "relation_to_type": "type", "validated": true, "ani": 79.4862, "matched_fragments": 633, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium jicamae", "strain": "strain=PAC68", "accession": "GCA_001440395.1", "taxid": 280332, "species_taxid": 280332, "relation_to_type": "type", "validated": true, "ani": 79.4595, "matched_fragments": 633, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cytisi", "strain": "strain=CTAW11", "accession": "GCA_008123515.1", "taxid": 515489, "species_taxid": 515489, "relation_to_type": "type", "validated": true, "ani": 79.3909, "matched_fragments": 611, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=LMG 26795", "accession": "GCA_900116675.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 79.3392, "matched_fragments": 654, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium arachidis", "strain": "strain=CCBAU 051107", "accession": "GCA_015291705.1", "taxid": 858423, "species_taxid": 858423, "relation_to_type": "type", "validated": true, "ani": 79.3224, "matched_fragments": 655, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium guangxiense", "strain": "strain=CCBAU 53363", "accession": "GCA_004114915.1", "taxid": 1325115, "species_taxid": 1325115, "relation_to_type": "type", "validated": true, "ani": 79.3072, "matched_fragments": 643, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopseudomonas faecalis", "strain": "strain=JCM 11668", "accession": "GCA_003217325.1", "taxid": 99655, "species_taxid": 99655, "relation_to_type": "type", "validated": true, "ani": 79.2394, "matched_fragments": 446, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium valentinum", "strain": "strain=LmjM3", "accession": "GCA_001440405.1", "taxid": 1518501, "species_taxid": 1518501, "relation_to_type": "type", "validated": true, "ani": 79.1879, "matched_fragments": 582, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia broomeae", "strain": "strain=ATCC 49717", "accession": "GCA_000314675.2", "taxid": 56946, "species_taxid": 56946, "relation_to_type": "type", "validated": true, "ani": 79.1072, "matched_fragments": 469, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afipia massiliensis", "strain": "strain=DSM 17498", "accession": "GCA_014203115.1", "taxid": 211460, "species_taxid": 211460, "relation_to_type": "type", "validated": true, "ani": 78.9087, "matched_fragments": 465, "total_fragments": 1273, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 76.84, "contamination": 4.69, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004173095.1", "gtdb_species": "s__Tardiphaga sp004173095", "ani": 91.22, "matched_fragments": 859, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "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_018279705.1", "gtdb_species": "s__Tardiphaga sp018279705", "ani": 84.7659, "matched_fragments": 951, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "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_002256345.1", "gtdb_species": "s__Tardiphaga sp002256345", "ani": 84.7394, "matched_fragments": 988, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "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_013359755.1", "gtdb_species": "s__Tardiphaga robiniae", "ani": 82.4225, "matched_fragments": 885, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.54", "min_intra_species_ani": "96.42", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001618955.1", "gtdb_species": "s__Tardiphaga robiniae_A", "ani": 82.2772, "matched_fragments": 877, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "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_003096755.1", "gtdb_species": "s__Tardiphaga sp003096755", "ani": 82.2381, "matched_fragments": 890, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "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_900114605.1", "gtdb_species": "s__Tardiphaga sp900114605", "ani": 82.2151, "matched_fragments": 897, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008329525.1", "gtdb_species": "s__Tardiphaga sp008329525", "ani": 82.1416, "matched_fragments": 884, "total_fragments": 1273, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga", "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": 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__Alphaproteobacteria", "o__Rhizobiales", "f__Xanthobacteraceae", "g__Tardiphaga", "s__Tardiphaga sp026400425" ], "_genome_taxon": [ "Hyphomicrobiales", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Xanthobacteraceae", "g__Tardiphaga", "s__Tardiphaga sp026400425", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Xanthobacteraceae", "Tardiphaga", "Tardiphaga", "sp026400425" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }