{ "type": "genome", "identifier": "GCA_012032175.1", "organism": "Rhodomicrobium sp.", "title": "Rhodomicrobium sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Wisconsin, Madison", "publication": [ {} ], "properties": { "assembly_accession": "GCA_012032175.1", "bioproject": "PRJNA612530", "biosample": "SAMN14376513", "wgs_master": "JAAURQ000000000.1", "refseq_category": "na", "taxid": "2720632", "species_taxid": "2720632", "organism_name": "Rhodomicrobium sp.", "infraspecific_name": "", "isolate": "RU_3_5", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/05", "asm_name": "ASM1203217v1", "submitter": "University of Wisconsin, Madison", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/032/175/GCA_012032175.1_ASM1203217v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-05", "dateModified": "2020-04-05", "datePublished": "2020-04-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodomicrobium sp." ], "sample_taxid": [ "2720632" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Africa:Cape Recife" ], "sample_host_location_id": [], "data_size": "0.957 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 65.51, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3359387", "Number of Sequences": "563", "Longest Sequences (bp)": "25447", "N50 (bp)": "6310", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.0", "Number of CDSs": "3335", "Average Protein Length": "235.2", "Coding Ratio (%)": "70.0", "Number of rRNAs": "0", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Kaistia adipata", "strain": "strain=DSM 17808", "accession": "GCA_000423225.1", "taxid": 166954, "species_taxid": 166954, "relation_to_type": "type", "validated": true, "ani": 77.0628, "matched_fragments": 106, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodomicrobium lacus", "strain": "strain=JA980", "accession": "GCA_003992725.1", "taxid": 2498452, "species_taxid": 2498452, "relation_to_type": "type", "validated": true, "ani": 77.0308, "matched_fragments": 108, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phreatobacter oligotrophus", "strain": "strain=DSM 25521", "accession": "GCA_003046185.1", "taxid": 1122261, "species_taxid": 1122261, "relation_to_type": "type", "validated": true, "ani": 76.8787, "matched_fragments": 121, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphiplicatus metriothermophilus", "strain": "strain=DSM 105738", "accession": "GCA_014199495.1", "taxid": 1519374, "species_taxid": 1519374, "relation_to_type": "type", "validated": true, "ani": 76.8741, "matched_fragments": 99, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methyloligella halotolerans", "strain": "strain=VKM B-2706", "accession": "GCA_001708935.1", "taxid": 1177755, "species_taxid": 1177755, "relation_to_type": "type", "validated": true, "ani": 76.8658, "matched_fragments": 86, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodomicrobium udaipurense", "strain": "strain=JA643", "accession": "GCA_000636015.1", "taxid": 1202716, "species_taxid": 1202716, 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76.843, "matched_fragments": 105, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobium orientis", "strain": "strain=DSM 11290", "accession": "GCA_003258835.1", "taxid": 34017, "species_taxid": 34017, "relation_to_type": "type", "validated": true, "ani": 76.8344, "matched_fragments": 125, "total_fragments": 893, "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": 76.8088, "matched_fragments": 132, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidamorphus gemmatus", "strain": "strain=DSM 19345", "accession": "GCA_004346195.1", "taxid": 747076, "species_taxid": 747076, "relation_to_type": "type", "validated": true, "ani": 76.7887, "matched_fragments": 106, "total_fragments": 893, "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": 76.7776, "matched_fragments": 132, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodomicrobium udaipurense", "strain": "strain=JA643", "accession": "GCA_016461795.1", "taxid": 1202716, "species_taxid": 1202716, "relation_to_type": "type", "validated": true, "ani": 76.7772, "matched_fragments": 118, "total_fragments": 893, "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": 76.7458, "matched_fragments": 149, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylosinus sporium", "strain": "strain=DSM 17706", "accession": "GCA_009811675.1", "taxid": 428, "species_taxid": 428, "relation_to_type": "type", "validated": true, "ani": 76.7196, "matched_fragments": 105, "total_fragments": 893, "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": 76.7109, "matched_fragments": 126, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomicrobium album", "strain": "strain=XQ2", "accession": "GCA_009708035.1", "taxid": 2665159, "species_taxid": 2665159, "relation_to_type": "type", "validated": true, "ani": 76.6838, "matched_fragments": 115, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dichotomicrobium thermohalophilum", "strain": "strain=DSM 5002", "accession": "GCA_003550175.1", "taxid": 933063, "species_taxid": 933063, "relation_to_type": "type", "validated": true, "ani": 76.6612, "matched_fragments": 116, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hyphomicrobium zavarzinii", "strain": "strain=ZV-622", "accession": "GCA_000383415.1", "taxid": 48292, "species_taxid": 48292, "relation_to_type": "type", "validated": true, "ani": 76.6488, "matched_fragments": 109, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azorhizobium caulinodans", "strain": "strain=ORS 571", "accession": "GCA_000010525.1", "taxid": 7, "species_taxid": 7, "relation_to_type": "type", "validated": true, "ani": 76.6477, "matched_fragments": 93, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter aminoxidans", "strain": "strain=ATCC BAA-299", "accession": "GCA_023571765.1", "taxid": 186280, "species_taxid": 186280, "relation_to_type": "type", "validated": true, "ani": 76.5837, "matched_fragments": 108, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kaustia mangrovi", "strain": "strain=R1DC25", "accession": "GCA_015482775.1", "taxid": 2593653, "species_taxid": 2593653, "relation_to_type": "type", "validated": true, "ani": 76.5715, "matched_fragments": 143, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kaistia soli", "strain": "strain=DSM 19436", "accession": "GCA_900129325.1", "taxid": 446684, "species_taxid": 446684, "relation_to_type": "type", "validated": true, "ani": 76.4987, "matched_fragments": 97, "total_fragments": 893, "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": 76.479, "matched_fragments": 135, "total_fragments": 893, "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": 76.4271, "matched_fragments": 126, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoblastus sphagnicola", "strain": "strain=DSM 16996", "accession": "GCA_002937075.1", "taxid": 333368, "species_taxid": 333368, "relation_to_type": "type", "validated": true, "ani": 76.2992, "matched_fragments": 109, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter oligotrophicus", "strain": "strain=29k", "accession": "GCA_008364685.1", "taxid": 2607286, "species_taxid": 2607286, "relation_to_type": "type", "validated": true, "ani": 76.2341, "matched_fragments": 99, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquisalinus flavus", "strain": "strain=CGMCC 1.12921", "accession": "GCA_014640095.1", "taxid": 1526572, "species_taxid": 1526572, "relation_to_type": "type", "validated": true, "ani": 76.1478, "matched_fragments": 63, "total_fragments": 893, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 65.51, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002198715.1", "gtdb_species": "s__R-RK-3 sp002198715", "ani": 79.1782, "matched_fragments": 402, "total_fragments": 893, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodomicrobiaceae;g__R-RK-3", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" 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