{ "type": "genome", "identifier": "GCA_026400535.1", "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_026400535.1", "bioproject": "PRJNA852163", "biosample": "SAMN30026355", "wgs_master": "JAPLOU000000000.1", "refseq_category": "na", "taxid": "1909294", "species_taxid": "1909294", "organism_name": "Hyphomicrobiales bacterium", "infraspecific_name": "", "isolate": "LacPavin_0818_WC50_MAG_65_19", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/24", "asm_name": "ASM2640053v1", "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/026/400/535/GCA_026400535.1_ASM2640053v1", "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": "1.057 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 85.71, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3791592", "Number of Sequences": "100", "Longest Sequences (bp)": "287158", "N50 (bp)": "72590", "Gap Ratio (%)": "0.000923", "GCcontent (%)": "64.6", "Number of CDSs": "3631", "Average Protein Length": "303.2", "Coding Ratio (%)": "87.1", "Number of rRNAs": "0", "Number of tRNAs": "42", "Number of CRISPRs": "2" }, "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": 78.1319, "matched_fragments": 440, "total_fragments": 1216, "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": 78.0108, "matched_fragments": 377, "total_fragments": 1216, "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": 77.9089, "matched_fragments": 423, "total_fragments": 1216, "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": 77.8624, "matched_fragments": 417, "total_fragments": 1216, "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": 77.8441, "matched_fragments": 423, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea lathyri", "strain": "strain=DSM 26656", "accession": "GCA_900108245.1", "taxid": 1036778, "species_taxid": 1036778, "relation_to_type": "type", "validated": true, "ani": 77.7287, "matched_fragments": 378, "total_fragments": 1216, "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": 77.4675, "matched_fragments": 298, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga thermotolerans", "strain": "strain=HR1", "accession": "GCA_009363855.1", "taxid": 2651334, "species_taxid": 2651334, "relation_to_type": "type", "validated": true, "ani": 77.225, "matched_fragments": 205, "total_fragments": 1216, "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": 77.1751, "matched_fragments": 194, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelatococcus composti", "strain": "strain=DSM 101465", "accession": "GCA_018398355.1", "taxid": 1743235, "species_taxid": 1743235, "relation_to_type": "type", "validated": true, "ani": 77.1436, "matched_fragments": 239, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium dankookense", "strain": "strain=SW08-7", "accession": "GCA_902141855.1", "taxid": 560405, "species_taxid": 560405, "relation_to_type": "type", "validated": true, "ani": 77.1386, "matched_fragments": 238, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium dankookense", "strain": "strain=DSM 22415", "accession": "GCA_022179165.1", "taxid": 560405, "species_taxid": 560405, "relation_to_type": "type", "validated": true, "ani": 77.1329, "matched_fragments": 222, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga guangxiensis", "strain": "strain=CGMCC 1.7666", "accession": "GCA_900102135.1", "taxid": 549386, "species_taxid": 549386, "relation_to_type": "type", "validated": true, "ani": 77.0642, "matched_fragments": 178, "total_fragments": 1216, "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": 77.0639, "matched_fragments": 270, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium gregans", "strain": "strain=NBRC 103626", "accession": "GCA_022179245.1", "taxid": 374424, "species_taxid": 374424, "relation_to_type": "type", "validated": true, "ani": 76.9881, "matched_fragments": 207, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga makkahensis", "strain": "strain=KCTC 23863", "accession": "GCA_009830105.1", "taxid": 1128670, "species_taxid": 1128670, "relation_to_type": "type", "validated": true, "ani": 76.916, "matched_fragments": 184, "total_fragments": 1216, "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": 76.9079, "matched_fragments": 256, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylorubrum rhodesianum", "strain": "strain=DSM 5687", "accession": "GCA_014199985.1", "taxid": 29427, "species_taxid": 29427, "relation_to_type": "type", "validated": true, "ani": 76.8189, "matched_fragments": 204, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium frigidaeris", "strain": "strain=JCM 32048", "accession": "GCA_022179185.1", "taxid": 2038277, "species_taxid": 2038277, "relation_to_type": "type", "validated": true, "ani": 76.7878, "matched_fragments": 274, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelatococcus asaccharovorans", "strain": "strain=DSM 6462", "accession": "GCA_003201475.1", "taxid": 28210, "species_taxid": 28210, "relation_to_type": "type", "validated": true, "ani": 76.705, "matched_fragments": 199, "total_fragments": 1216, "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": 76.684, "matched_fragments": 287, "total_fragments": 1216, "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": 76.6708, "matched_fragments": 244, "total_fragments": 1216, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 85.71, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001713455.1", "gtdb_species": "s__Bosea sp001713455", "ani": 78.3142, "matched_fragments": 445, "total_fragments": 1216, "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_011764485.1", "gtdb_species": "s__Bosea sp011764485", "ani": 78.1964, "matched_fragments": 374, "total_fragments": 1216, "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_002279705.1", "gtdb_species": "s__Bosea sp002279705", "ani": 78.1755, "matched_fragments": 398, "total_fragments": 1216, "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": "GCA_900470775.1", "gtdb_species": "s__Bosea sp900470775", "ani": 78.1479, "matched_fragments": 402, "total_fragments": 1216, "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_001295925.1", "gtdb_species": "s__Bosea sp001295925", "ani": 78.1325, "matched_fragments": 358, "total_fragments": 1216, "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_003351345.1", "gtdb_species": "s__Bosea caraganae", "ani": 78.1156, "matched_fragments": 442, "total_fragments": 1216, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001426225.1", "gtdb_species": "s__Bosea sp001426225", "ani": 78.0779, "matched_fragments": 410, "total_fragments": 1216, "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_001898115.1", "gtdb_species": "s__Bosea sp001898115", "ani": 78.0753, "matched_fragments": 355, "total_fragments": 1216, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.43", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001509835.1", "gtdb_species": "s__Bosea sp001509835", "ani": 78.0725, "matched_fragments": 422, "total_fragments": 1216, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000745475.1", "gtdb_species": "s__Bosea vestrisii", "ani": 77.9899, "matched_fragments": 397, "total_fragments": 1216, "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_003248805.1", "gtdb_species": "s__Bosea sp003248805", "ani": 77.9734, "matched_fragments": 371, "total_fragments": 1216, "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_004341515.1", "gtdb_species": "s__Bosea sp004341515", "ani": 77.9254, "matched_fragments": 430, "total_fragments": 1216, "gtdb_taxonomy": 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