{ "type": "genome", "identifier": "GCA_022844485.1", "organism": "Xanthobacteraceae bacterium", "title": "Xanthobacteraceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Northeastern University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022844485.1", "bioproject": "PRJNA764197", "biosample": "SAMN21474276", "wgs_master": "JALHLQ000000000.1", "refseq_category": "na", "taxid": "2021379", "species_taxid": "2021379", "organism_name": "Xanthobacteraceae bacterium", "infraspecific_name": "", "isolate": "Bin_23_12", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/08", "asm_name": "ASM2284448v1", "submitter": "Northeastern University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/844/485/GCA_022844485.1_ASM2284448v1", "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": "2022-04-08", "dateModified": "2022-04-08", "datePublished": "2022-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthobacteraceae bacterium" ], "sample_taxid": [ "2021379" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Ann Arbor, Michigan" ], "sample_host_location_id": [], "data_size": "1.153 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4147226", "Number of Sequences": "44", "Longest Sequences (bp)": "540368", "N50 (bp)": "141350", "Gap Ratio (%)": "0.001447", "GCcontent (%)": "64.1", "Number of CDSs": "3997", "Average Protein Length": "309.4", "Coding Ratio (%)": "89.5", "Number of rRNAs": "1", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodoplanes elegans", "strain": "strain=DSM 11907", "accession": "GCA_016653355.1", "taxid": 29408, "species_taxid": 29408, "relation_to_type": "type", "validated": true, "ani": 77.6312, "matched_fragments": 383, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoplanes elegans", "strain": "strain=DSM 11907", "accession": "GCA_003258805.1", "taxid": 29408, "species_taxid": 29408, "relation_to_type": "type", "validated": true, "ani": 77.5407, "matched_fragments": 342, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoplanes piscinae", "strain": "strain=DSM 19946", "accession": "GCA_003258855.1", "taxid": 444923, "species_taxid": 444923, "relation_to_type": "type", "validated": true, "ani": 77.4945, "matched_fragments": 336, "total_fragments": 1365, "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": 77.4198, "matched_fragments": 340, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium betae", "strain": "strain=CECT 5829", "accession": "GCA_024806875.1", "taxid": 244734, "species_taxid": 244734, "relation_to_type": "type", "validated": true, "ani": 77.381, "matched_fragments": 316, "total_fragments": 1365, "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": 77.341, "matched_fragments": 316, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoplanes roseus", "strain": "strain=DSM 5909", "accession": "GCA_003258865.1", "taxid": 29409, "species_taxid": 29409, "relation_to_type": "type", "validated": true, "ani": 77.324, "matched_fragments": 367, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diazoefficiens", "strain": "strain=USDA 110", "accession": "GCA_001642675.1", "taxid": 1355477, "species_taxid": 1355477, "relation_to_type": "type", "validated": true, "ani": 77.3214, "matched_fragments": 333, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Starkeya novella", "strain": "strain=DSM 506", "accession": "GCA_000092925.1", "taxid": 921, "species_taxid": 921, "relation_to_type": "type", "validated": true, "ani": 77.3174, "matched_fragments": 254, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diazoefficiens", "strain": "strain=USDA110", "accession": "GCA_000011365.1", "taxid": 1355477, "species_taxid": 1355477, "relation_to_type": "type", "validated": true, "ani": 77.2798, "matched_fragments": 334, "total_fragments": 1365, "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": 77.2726, "matched_fragments": 308, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium icense", "strain": "strain=LMTR 13", "accession": "GCA_001693385.1", "taxid": 1274631, "species_taxid": 1274631, "relation_to_type": "type", "validated": true, "ani": 77.2667, "matched_fragments": 283, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium niftali", "strain": "strain=CNPSo 3448", "accession": "GCA_004571025.1", "taxid": 2560055, "species_taxid": 2560055, "relation_to_type": "type", "validated": true, "ani": 77.2497, "matched_fragments": 345, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium diversitatis", "strain": "strain=CNPSo 4019", "accession": "GCA_016031635.1", "taxid": 2755406, "species_taxid": 2755406, "relation_to_type": "type", "validated": true, "ani": 77.2309, "matched_fragments": 315, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium pachyrhizi", "strain": "strain=PAC 48", "accession": "GCA_001189245.1", "taxid": 280333, "species_taxid": 280333, "relation_to_type": "type", "validated": true, "ani": 77.2277, "matched_fragments": 338, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium viridifuturi", "strain": "strain=SEMIA 690", "accession": "GCA_001238275.1", "taxid": 1654716, "species_taxid": 1654716, "relation_to_type": "type", "validated": true, "ani": 77.2051, "matched_fragments": 344, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium acaciae", "strain": "strain=10BB", "accession": "GCA_020889785.1", "taxid": 2683706, "species_taxid": 2683706, "relation_to_type": "type", "validated": true, "ani": 77.202, "matched_fragments": 320, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium quebecense", "strain": "strain=66S1MB, /ecotype=symbiovar septentrionalis", "accession": "GCA_013373795.3", "taxid": 2748629, "species_taxid": 2748629, "relation_to_type": "type", "validated": true, "ani": 77.1647, "matched_fragments": 328, "total_fragments": 1365, "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": 77.1079, "matched_fragments": 285, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium shewense", "strain": "strain=ERR11", "accession": "GCA_900094605.1", "taxid": 1761772, "species_taxid": 1761772, "relation_to_type": "type", "validated": true, "ani": 77.0982, "matched_fragments": 321, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variibacter gotjawalensis", "strain": "strain=CECT 8514", "accession": "GCA_011761465.1", "taxid": 1333996, "species_taxid": 1333996, "relation_to_type": "type", "validated": true, "ani": 77.0326, "matched_fragments": 240, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variibacter gotjawalensis", "strain": "strain=GJW-30", "accession": "GCA_002355335.1", "taxid": 1333996, "species_taxid": 1333996, "relation_to_type": "type", "validated": true, "ani": 77.0287, "matched_fragments": 245, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Variibacter gotjawalensis", "strain": "strain=DSM 29671", "accession": "GCA_004216635.1", "taxid": 1333996, "species_taxid": 1333996, "relation_to_type": "type", "validated": true, "ani": 77.0097, "matched_fragments": 244, "total_fragments": 1365, "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": 76.7064, "matched_fragments": 263, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Terrihabitans soli", "strain": "strain=IZ6", "accession": "GCA_014191545.1", "taxid": 708113, "species_taxid": 708113, "relation_to_type": "type", "validated": true, "ani": 76.6445, "matched_fragments": 155, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor alexandrii", "strain": "strain=Z3-1", "accession": "GCA_004000215.1", "taxid": 2448161, "species_taxid": 2448161, "relation_to_type": "type", "validated": true, "ani": 76.3843, "matched_fragments": 176, "total_fragments": 1365, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_003105195.1", "gtdb_species": "s__FEB-22 sp003105195", "ani": 78.2286, "matched_fragments": 396, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22", "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_019187085.1", "gtdb_species": "s__Pseudorhodoplanes sp019187085", "ani": 78.0207, "matched_fragments": 369, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.90", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_005884685.1", "gtdb_species": "s__PALSA-894 sp005884685", "ani": 77.9471, "matched_fragments": 402, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894", "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_003152455.1", "gtdb_species": "s__Pseudolabrys sp003152455", "ani": 77.932, "matched_fragments": 323, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys", "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_013388965.1", "gtdb_species": "s__Pseudorhodoplanes sp013388965", "ani": 77.9088, "matched_fragments": 332, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes", "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_008933495.1", "gtdb_species": "s__Pseudorhodoplanes sp008933495", "ani": 77.8922, "matched_fragments": 277, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes", "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_000293785.1", "gtdb_species": "s__Rhodoplanes sp000293785", "ani": 77.8214, "matched_fragments": 329, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes", "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_016653355.1", "gtdb_species": "s__Rhodoplanes elegans", "ani": 77.6641, "matched_fragments": 379, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.89", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017304555.1", "gtdb_species": "s__JAFKKS01 sp017304555", "ani": 77.6605, "matched_fragments": 250, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__JAFKKS01", "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_001899285.1", "gtdb_species": "s__Pseudolabrys sp001899285", "ani": 77.6087, "matched_fragments": 340, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009720755.1", "gtdb_species": "s__Rhodoplanes serenus", "ani": 77.5504, "matched_fragments": 373, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "97.48", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_009377755.1", "gtdb_species": "s__WHTM01 sp009377755", "ani": 77.5389, "matched_fragments": 335, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__WHTM01", "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_005884745.1", "gtdb_species": "s__AP-16 sp005884745", "ani": 77.4873, "matched_fragments": 254, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__AP-16", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016793685.1", "gtdb_species": "s__Rhodoplanes sp016793685", "ani": 77.434, "matched_fragments": 145, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes", "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_013377085.1", "gtdb_species": "s__Rhodoplanes sp013377085", "ani": 77.4329, "matched_fragments": 400, "total_fragments": 1365, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes", "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_003140315.1", 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