{ "type": "genome", "identifier": "GCA_005882425.1", "organism": "Alphaproteobacteria bacterium", "title": "Alphaproteobacteria 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_005882425.1", "bioproject": "PRJNA449266", "biosample": "SAMN11380278", "wgs_master": "VAZY00000000.1", "refseq_category": "na", "taxid": "1913988", "species_taxid": "1913988", "organism_name": "Alphaproteobacteria bacterium", "infraspecific_name": "", "isolate": "AP_20", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/29", "asm_name": "ASM588242v1", "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/005/882/425/GCA_005882425.1_ASM588242v1", "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": "2019-05-29", "dateModified": "2019-05-29", "datePublished": "2019-05-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Alphaproteobacteria bacterium" ], "sample_taxid": [ "1913988" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Angelo Coast Range Reserve, CA" ], "sample_host_location_id": [], "data_size": "1.022 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 81.02, "contamination": 4.55, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3704385", "Number of Sequences": "424", "Longest Sequences (bp)": "49997", "N50 (bp)": "12731", "Gap Ratio (%)": "0.421986", "GCcontent (%)": "66.3", "Number of CDSs": "3293", "Average Protein Length": "280.2", "Coding Ratio (%)": "74.7", "Number of rRNAs": "0", "Number of tRNAs": "30", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodoplanes piscinae", "strain": "strain=DSM 19946", "accession": "GCA_003258855.1", "taxid": 444923, "species_taxid": 444923, "relation_to_type": "type", "validated": true, "ani": 78.3506, "matched_fragments": 316, "total_fragments": 1022, "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": 78.1683, "matched_fragments": 348, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blastochloris tepida", "strain": "strain=GI", "accession": "GCA_003966715.1", "taxid": 2233851, "species_taxid": 2233851, "relation_to_type": "type", "validated": true, "ani": 78.1557, "matched_fragments": 261, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoplanes elegans", "strain": "strain=DSM 11907", "accession": "GCA_016653355.1", "taxid": 29408, "species_taxid": 29408, "relation_to_type": "type", "validated": true, "ani": 78.0528, "matched_fragments": 376, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopseudomonas rhenobacensis", "strain": "strain=DSM 12706", "accession": "GCA_014203125.1", "taxid": 87461, "species_taxid": 87461, "relation_to_type": "type", "validated": true, "ani": 78.024, "matched_fragments": 317, "total_fragments": 1022, "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": 77.9984, "matched_fragments": 354, "total_fragments": 1022, "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": 77.9814, "matched_fragments": 332, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blastochloris viridis", "strain": "strain=DSM 133", "accession": "GCA_001548155.2", "taxid": 1079, "species_taxid": 1079, "relation_to_type": "type", "validated": true, "ani": 77.951, "matched_fragments": 256, "total_fragments": 1022, "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": 77.9359, "matched_fragments": 358, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Blastochloris viridis", "strain": "strain=ATCC 19567", "accession": "GCA_001402875.1", "taxid": 1079, "species_taxid": 1079, "relation_to_type": "type", "validated": true, "ani": 77.8925, "matched_fragments": 261, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium aeschynomenes", "strain": "strain=83002", "accession": "GCA_013178945.1", "taxid": 2734909, "species_taxid": 2734909, "relation_to_type": "type", "validated": true, "ani": 77.8601, "matched_fragments": 327, "total_fragments": 1022, "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": 77.84, "matched_fragments": 327, "total_fragments": 1022, "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": 77.8264, "matched_fragments": 394, "total_fragments": 1022, "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": 77.8251, "matched_fragments": 361, "total_fragments": 1022, "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": 77.7902, "matched_fragments": 352, "total_fragments": 1022, "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": 77.7702, "matched_fragments": 344, "total_fragments": 1022, "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": 77.739, "matched_fragments": 357, "total_fragments": 1022, "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": 77.7011, "matched_fragments": 308, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium cosmicum", "strain": "strain=58S1", "accession": "GCA_007290395.1", "taxid": 1404864, "species_taxid": 1404864, "relation_to_type": "type", "validated": true, "ani": 77.6995, "matched_fragments": 337, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium canariense", "strain": "strain=BTA-1", "accession": "GCA_019402665.1", "taxid": 255045, "species_taxid": 255045, "relation_to_type": "suspected-type", "validated": true, "ani": 77.6686, "matched_fragments": 345, "total_fragments": 1022, "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": 77.6179, "matched_fragments": 305, "total_fragments": 1022, "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": 77.5255, "matched_fragments": 314, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium murdochi", "strain": "strain=WSM 1741", "accession": "GCA_000472965.1", "taxid": 1038859, "species_taxid": 1038859, "relation_to_type": "type", "validated": true, "ani": 77.5225, "matched_fragments": 297, "total_fragments": 1022, "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": 77.5199, "matched_fragments": 295, "total_fragments": 1022, "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": 77.4625, "matched_fragments": 371, "total_fragments": 1022, "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": 77.4278, "matched_fragments": 327, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelatococcus caeni", "strain": "strain=DSM 103737", "accession": "GCA_014196925.1", "taxid": 1348468, "species_taxid": 1348468, "relation_to_type": "type", "validated": true, "ani": 77.423, "matched_fragments": 269, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium isbiliense", "strain": "strain=DSM 17168", "accession": "GCA_022179325.1", "taxid": 315478, "species_taxid": 315478, "relation_to_type": "type", "validated": true, "ani": 76.8241, "matched_fragments": 291, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquamicrobium defluvii", "strain": "strain=DSM 11603", "accession": "GCA_004363725.1", "taxid": 69279, "species_taxid": 69279, "relation_to_type": "type", "validated": true, "ani": 76.7255, "matched_fragments": 134, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylosinus trichosporium", "strain": "strain=OB3b", "accession": "GCA_000178815.2", "taxid": 426, "species_taxid": 426, "relation_to_type": "type", "validated": true, "ani": 76.6082, "matched_fragments": 204, "total_fragments": 1022, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afifella marina", "strain": "strain=DSM 2698", "accession": "GCA_900102695.1", "taxid": 1080, "species_taxid": 1080, 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"total_fragments": 1022, "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": "conclusive" }, { "accession": "GCA_003105195.1", "gtdb_species": "s__FEB-22 sp003105195", "ani": 79.0245, "matched_fragments": 358, "total_fragments": 1022, "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_004297465.1", "gtdb_species": "s__SCUB01 sp004297465", "ani": 78.5643, "matched_fragments": 299, "total_fragments": 1022, "gtdb_taxonomy": 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