{ "type": "genome", "identifier": "GCA_026400515.1", "organism": "Hyphomicrobiales bacterium", "title": "Hyphomicrobiales bacterium", "description": "derived from metagenome; fragmented assembly; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Jill Banfield's Lab at Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_026400515.1", "bioproject": "PRJNA852163", "biosample": "SAMN30026358", "wgs_master": "JAPLOX000000000.1", "refseq_category": "na", "taxid": "1909294", "species_taxid": "1909294", "organism_name": "Hyphomicrobiales bacterium", "infraspecific_name": "", "isolate": "LacPavin_0818_WC50_MAG_59_6", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/24", "asm_name": "ASM2640051v1", "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/026/400/515/GCA_026400515.1_ASM2640051v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly; 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": "0.697 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 84.72, "contamination": 0.52, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2463447", "Number of Sequences": "567", "Longest Sequences (bp)": "30593", "N50 (bp)": "5303", "Gap Ratio (%)": "0.241775", "GCcontent (%)": "58.7", "Number of CDSs": "2044", "Average Protein Length": "267.6", "Coding Ratio (%)": "66.6", "Number of rRNAs": "0", "Number of tRNAs": "21", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bosea psychrotolerans", "strain": "strain=1131", "accession": "GCA_002917105.1", "taxid": 1871628, "species_taxid": 1871628, "relation_to_type": "type", "validated": true, "ani": 76.59, "matched_fragments": 90, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoblastus acidophilus", "strain": "strain=DSM 137", "accession": "GCA_002937135.1", "taxid": 1074, "species_taxid": 1074, "relation_to_type": "suspected-type", "validated": true, "ani": 76.4821, "matched_fragments": 73, "total_fragments": 513, "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": 76.4634, "matched_fragments": 81, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoblastus acidophilus", "strain": "strain=DSM 137", "accession": "GCA_900187365.1", "taxid": 1074, "species_taxid": 1074, "relation_to_type": "suspected-type", "validated": true, "ani": 76.4562, "matched_fragments": 74, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoblastus acidophilus", "strain": "strain=DSM 137", "accession": "GCA_003258765.1", "taxid": 1074, "species_taxid": 1074, "relation_to_type": "suspected-type", "validated": true, "ani": 76.4548, "matched_fragments": 74, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phreatobacter stygius", "strain": "strain=KCTC 52518", "accession": "GCA_005144885.1", "taxid": 1940610, "species_taxid": 1940610, "relation_to_type": "type", "validated": true, "ani": 76.4252, "matched_fragments": 103, "total_fragments": 513, "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": 76.4169, "matched_fragments": 71, "total_fragments": 513, "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": 76.3772, "matched_fragments": 50, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium ottawaense", "strain": "strain=OO99", "accession": "GCA_002278135.2", "taxid": 931866, "species_taxid": 931866, "relation_to_type": "type", "validated": true, "ani": 76.3531, "matched_fragments": 65, "total_fragments": 513, "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": 76.3353, "matched_fragments": 56, "total_fragments": 513, "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": 76.2728, "matched_fragments": 90, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saliniramus fredricksonii", "strain": "strain=HL-109", "accession": "GCA_900094735.1", "taxid": 1653334, "species_taxid": 1653334, "relation_to_type": "type", "validated": true, "ani": 76.2625, "matched_fragments": 74, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Camelimonas fluminis", "strain": "strain=KCTC 42282", "accession": "GCA_014656355.1", "taxid": 1576911, "species_taxid": 1576911, "relation_to_type": "type", "validated": true, "ani": 76.1943, "matched_fragments": 54, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelatococcus sambhunathii", "strain": "strain=DSM 18167", "accession": "GCA_001418005.1", "taxid": 363953, "species_taxid": 363953, "relation_to_type": "type", "validated": true, "ani": 76.1342, "matched_fragments": 52, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelatococcus sambhunathii", "strain": "strain=DSM 18167", "accession": "GCA_001517345.1", "taxid": 363953, "species_taxid": 363953, "relation_to_type": "type", "validated": true, "ani": 76.1342, "matched_fragments": 52, "total_fragments": 513, "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": 76.1248, "matched_fragments": 91, "total_fragments": 513, "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": 76.0867, "matched_fragments": 77, "total_fragments": 513, "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": 76.0798, "matched_fragments": 71, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alsobacter soli", "strain": "strain=SH9", "accession": "GCA_003004785.1", "taxid": 2109933, "species_taxid": 2109933, "relation_to_type": "type", "validated": true, "ani": 76.0754, "matched_fragments": 78, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium jarvisii", "strain": "strain=LMG 28313", "accession": "GCA_003601985.1", "taxid": 1777867, "species_taxid": 1777867, "relation_to_type": "type", "validated": true, "ani": 76.0753, "matched_fragments": 56, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium jarvisii", "strain": "strain=ATCC 33669", "accession": "GCA_013170785.1", "taxid": 1777867, "species_taxid": 1777867, "relation_to_type": "type", "validated": true, "ani": 76.0752, "matched_fragments": 56, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microvirga aerilata", "strain": "strain=5420S-16", "accession": "GCA_016743775.1", "taxid": 670292, "species_taxid": 670292, "relation_to_type": "type", "validated": true, "ani": 76.0216, "matched_fragments": 62, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bosea caraganae", "strain": "strain=RCAM 04680", "accession": "GCA_003351345.1", "taxid": 2763117, "species_taxid": 2763117, "relation_to_type": "type", "validated": true, "ani": 75.9384, "matched_fragments": 93, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001517385.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 75.7827, "matched_fragments": 58, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001418225.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 75.7827, "matched_fragments": 58, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kaistia hirudinis", "strain": "strain=DSM 25966", "accession": "GCA_014196455.1", "taxid": 1293440, "species_taxid": 1293440, "relation_to_type": "type", "validated": true, "ani": 75.7623, "matched_fragments": 54, "total_fragments": 513, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 84.72, "contamination": 0.52, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903930675.1", "gtdb_species": "s__CAIYZJ01 sp903930675", "ani": 98.3501, "matched_fragments": 464, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.85", "min_intra_species_ani": "97.85", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_903824185.1", "gtdb_species": "s__CAIYZJ01 sp903824185", "ani": 77.7061, "matched_fragments": 189, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.80", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_903900975.1", "gtdb_species": "s__CAIUPE01 sp903900975", "ani": 77.1236, "matched_fragments": 63, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIUPE01", "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_019083985.1", "gtdb_species": "s__TNE-4 sp019083985", "ani": 76.7832, "matched_fragments": 99, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__TNE-4", "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": "GCA_018882635.1", "gtdb_species": "s__TNE-4 sp018882635", "ani": 76.5773, "matched_fragments": 72, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__TNE-4", "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_900104955.1", "gtdb_species": "s__28-YEA-48 sp900104955", "ani": 76.4689, "matched_fragments": 70, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "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": 76.4634, "matched_fragments": 81, "total_fragments": 513, "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", 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{ "accession": "GCF_011777495.1", "gtdb_species": "s__Microvirga sp011777495", "ani": 76.3703, "matched_fragments": 54, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga", "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_002278135.2", "gtdb_species": "s__Bradyrhizobium ottawaense", "ani": 76.3531, "matched_fragments": 65, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_900473415.1", 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76.1758, "matched_fragments": 69, "total_fragments": 513, "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_008253865.1", "gtdb_species": "s__Bosea sp008253865", "ani": 76.1525, "matched_fragments": 92, "total_fragments": 513, "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": 76.1472, "matched_fragments": 67, "total_fragments": 513, "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_900156025.1", "gtdb_species": "s__Bosea sp900156025", "ani": 76.139, "matched_fragments": 83, "total_fragments": 513, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.08", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001741865.1", "gtdb_species": "s__Bosea vaviloviae", "ani": 76.1248, "matched_fragments": 91, "total_fragments": 513, "gtdb_taxonomy": 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