{ "type": "genome", "identifier": "GCA_026400565.1", "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_026400565.1", "bioproject": "PRJNA852163", "biosample": "SAMN30026356", "wgs_master": "JAPLOV000000000.1", "refseq_category": "na", "taxid": "1909294", "species_taxid": "1909294", "organism_name": "Hyphomicrobiales bacterium", "infraspecific_name": "", "isolate": "LacPavin_0818_WC50_MAG_65_8", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/24", "asm_name": "ASM2640056v1", "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/026/400/565/GCA_026400565.1_ASM2640056v1", "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": "0.959 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 89.58, "contamination": 8.33, "strain_heterogeneity": 50.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3442918", "Number of Sequences": "267", "Longest Sequences (bp)": "88031", "N50 (bp)": "21705", "Gap Ratio (%)": "0.060007", "GCcontent (%)": "64.6", "Number of CDSs": "3210", "Average Protein Length": "293.8", "Coding Ratio (%)": "82.2", "Number of rRNAs": "0", "Number of tRNAs": "38", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bosea caraganae", "strain": "strain=RCAM 04680", "accession": "GCA_003351345.1", "taxid": 2763117, "species_taxid": 2763117, "relation_to_type": "type", "validated": true, "ani": 78.1374, "matched_fragments": 427, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea thiooxidans", "strain": "strain=DSM 9653", "accession": "GCA_900168195.1", "taxid": 53254, "species_taxid": 53254, "relation_to_type": "type", "validated": true, "ani": 78.0838, "matched_fragments": 368, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea robiniae", "strain": "strain=DSM 26672", "accession": "GCA_900102525.1", "taxid": 1036780, "species_taxid": 1036780, "relation_to_type": "type", "validated": true, "ani": 78.0338, "matched_fragments": 373, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea vaviloviae", "strain": "strain=Vaf18", "accession": "GCA_001741865.1", "taxid": 1526658, "species_taxid": 1526658, "relation_to_type": "type", "validated": true, "ani": 77.7097, "matched_fragments": 397, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea psychrotolerans", "strain": "strain=1131", "accession": "GCA_002917105.1", "taxid": 1871628, "species_taxid": 1871628, "relation_to_type": "type", "validated": true, "ani": 77.6516, "matched_fragments": 400, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terricola", "strain": "strain=17Sr1-39", "accession": "GCA_006151805.1", "taxid": 2583531, "species_taxid": 2583531, "relation_to_type": "type", "validated": true, "ani": 77.3155, "matched_fragments": 278, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nonmethylotrophicum", "strain": "strain=6HR-1", "accession": "GCA_004745635.1", "taxid": 1141884, "species_taxid": 1141884, "relation_to_type": "type", "validated": true, "ani": 77.2719, "matched_fragments": 279, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga lotononidis", "strain": "strain=WSM3557", "accession": "GCA_000262405.1", "taxid": 864069, "species_taxid": 864069, "relation_to_type": "type", "validated": true, "ani": 77.2695, "matched_fragments": 230, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium indicum", "strain": "strain=SE2.11", "accession": "GCA_001043895.1", "taxid": 1775910, "species_taxid": 1775910, "relation_to_type": "type", "validated": true, "ani": 77.2523, "matched_fragments": 261, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga subterranea", "strain": "strain=DSM 14364", "accession": "GCA_003350535.1", "taxid": 186651, "species_taxid": 186651, "relation_to_type": "type", "validated": true, "ani": 77.2322, "matched_fragments": 236, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga lenta", "strain": "strain=SM9", "accession": "GCA_020532555.1", "taxid": 2881337, "species_taxid": 2881337, "relation_to_type": "type", "validated": true, "ani": 77.2311, "matched_fragments": 234, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phreatobacter cathodiphilus", "strain": "strain=S-12", "accession": "GCA_003008515.1", "taxid": 1868589, "species_taxid": 1868589, "relation_to_type": "type", "validated": true, "ani": 77.2007, "matched_fragments": 272, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium oryzihabitans", "strain": "strain=TER-1", "accession": "GCA_004004555.2", "taxid": 2499852, "species_taxid": 2499852, "relation_to_type": "type", "validated": true, "ani": 77.1804, "matched_fragments": 273, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga mediterraneensis", "strain": "strain=Marseille-Q2068", "accession": "GCA_013520865.1", "taxid": 2754695, "species_taxid": 2754695, "relation_to_type": "type", "validated": true, "ani": 77.1471, "matched_fragments": 217, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium currus", "strain": "strain=PR1016A", "accession": "GCA_003058325.1", "taxid": 2051553, "species_taxid": 2051553, "relation_to_type": "type", "validated": true, "ani": 77.1323, "matched_fragments": 292, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylorubrum podarium", "strain": "strain=DSM 15083", "accession": "GCA_022179745.1", "taxid": 200476, "species_taxid": 200476, "relation_to_type": "type", "validated": true, "ani": 77.027, "matched_fragments": 191, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga splendida", "strain": "strain=BT325", "accession": "GCA_016427565.1", "taxid": 2795727, "species_taxid": 2795727, "relation_to_type": "type", "validated": true, "ani": 77.0262, "matched_fragments": 233, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium jeotgali", "strain": "strain=LMG 23639", "accession": "GCA_022179345.1", "taxid": 381630, "species_taxid": 381630, "relation_to_type": "type", "validated": true, "ani": 77.0226, "matched_fragments": 180, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga calopogonii", "strain": "strain=CCBAU 65841", "accession": "GCA_003347665.1", "taxid": 2078013, "species_taxid": 2078013, "relation_to_type": "type", "validated": true, "ani": 76.9433, "matched_fragments": 213, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium iners", "strain": "strain=DSM 19015", "accession": "GCA_022179305.1", "taxid": 418707, "species_taxid": 418707, "relation_to_type": "type", "validated": true, "ani": 76.9375, "matched_fragments": 213, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nodulans", "strain": "strain=ORS 2060", "accession": "GCA_000022085.1", "taxid": 114616, "species_taxid": 114616, "relation_to_type": "type", "validated": true, "ani": 76.9265, "matched_fragments": 235, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga pakistanensis", "strain": "strain=NCCP-1258", "accession": "GCA_004458765.1", "taxid": 1682650, "species_taxid": 1682650, "relation_to_type": "type", "validated": true, "ani": 76.8838, "matched_fragments": 191, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium crusticola", "strain": "strain=KCTC 52305", "accession": "GCA_022179145.1", "taxid": 1697972, "species_taxid": 1697972, "relation_to_type": "type", "validated": true, "ani": 76.8822, "matched_fragments": 259, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter ferrooxidans", "strain": "strain=F8825", "accession": "GCA_004137355.1", "taxid": 2509717, "species_taxid": 2509717, "relation_to_type": "type", "validated": true, "ani": 76.3513, "matched_fragments": 113, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oricola indica", "strain": "strain=JL-62", "accession": "GCA_019966595.1", "taxid": 2872591, "species_taxid": 2872591, "relation_to_type": "type", "validated": true, "ani": 76.2145, "matched_fragments": 128, "total_fragments": 1014, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 89.58, "contamination": 8.33, "strain_heterogeneity": 50.0 }, "gtdb_result": [ { "accession": "GCF_001713455.1", "gtdb_species": "s__Bosea sp001713455", "ani": 78.2494, "matched_fragments": 427, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.00", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900112185.1", "gtdb_species": "s__Bosea sp900112185", "ani": 78.1335, "matched_fragments": 398, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_900466745.1", "gtdb_species": "s__Bosea sp900466745", "ani": 78.0898, "matched_fragments": 373, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_011764485.1", "gtdb_species": "s__Bosea sp011764485", "ani": 78.0659, "matched_fragments": 363, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_900102525.1", "gtdb_species": "s__Bosea robiniae", "ani": 78.0486, "matched_fragments": 372, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "97.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_001556125.1", "gtdb_species": "s__Bosea sp001556125", "ani": 78.0384, "matched_fragments": 406, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.92", "min_intra_species_ani": "96.82", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.77", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_008253865.1", "gtdb_species": "s__Bosea sp008253865", "ani": 77.9905, "matched_fragments": 368, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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_000745475.1", "gtdb_species": "s__Bosea vestrisii", "ani": 77.9829, "matched_fragments": 370, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_002279705.1", "gtdb_species": "s__Bosea sp002279705", "ani": 77.9517, "matched_fragments": 390, "total_fragments": 1014, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "99.41", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001298265.1", "gtdb_species": "s__Bosea vaviloviae_B", "ani": 77.8864, "matched_fragments": 387, "total_fragments": 1014, "gtdb_taxonomy": 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