{ "type": "genome", "identifier": "GCA_002869085.1", "organism": "Hyphomicrobiales bacterium", "title": "Hyphomicrobiales bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_002869085.1", "bioproject": "PRJNA387015", "biosample": "SAMN07982675", "wgs_master": "PKTQ00000000.1", "refseq_category": "na", "taxid": "1909294", "species_taxid": "1909294", "organism_name": "Hyphomicrobiales bacterium", "infraspecific_name": "", "isolate": "BM303", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/09", "asm_name": "ASM286908v1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/869/085/GCA_002869085.1_ASM286908v1", "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": "2018-01-09", "dateModified": "2018-01-09", "datePublished": "2018-01-09", "_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": [ "USA: Berkeley, CA, marina" ], "sample_host_location_id": [], "data_size": "0.986 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.46, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3529706", "Number of Sequences": "429", "Longest Sequences (bp)": "44321", "N50 (bp)": "11363", "Gap Ratio (%)": "0.005723", "GCcontent (%)": "61.3", "Number of CDSs": "3004", "Average Protein Length": "300.2", "Coding Ratio (%)": "76.7", "Number of rRNAs": "0", "Number of tRNAs": "39", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodobium orientis", "strain": "strain=DSM 11290", "accession": "GCA_003258835.1", "taxid": 34017, "species_taxid": 34017, "relation_to_type": "type", "validated": true, "ani": 76.9064, "matched_fragments": 206, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidicaulis marinus", "strain": "strain=MA2", "accession": "GCA_000739695.1", "taxid": 1333998, "species_taxid": 1333998, "relation_to_type": "type", "validated": true, "ani": 76.84, "matched_fragments": 122, "total_fragments": 955, "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": 76.7119, "matched_fragments": 134, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bauldia litoralis", "strain": "strain=ATCC 35022", "accession": "GCA_900104485.1", "taxid": 665467, "species_taxid": 665467, "relation_to_type": "type", "validated": true, "ani": 76.661, "matched_fragments": 143, "total_fragments": 955, "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": 76.655, "matched_fragments": 160, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ancylobacter aquaticus", "strain": "strain=DSM 101", "accession": "GCA_004339465.1", "taxid": 100, 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"validated": true, "ani": 76.4658, "matched_fragments": 74, "total_fragments": 955, "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": 76.4344, "matched_fragments": 140, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodoplanes sinuspersici", "strain": "strain=RIPI110", "accession": "GCA_002119765.1", "taxid": 1235591, "species_taxid": 1235591, "relation_to_type": "type", "validated": true, "ani": 76.434, "matched_fragments": 89, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudorhodoplanes sinuspersici", "strain": "strain=CECT 8374", "accession": "GCA_003610435.1", "taxid": 1235591, "species_taxid": 1235591, "relation_to_type": "type", "validated": true, "ani": 76.413, "matched_fragments": 90, "total_fragments": 955, "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": 76.3436, "matched_fragments": 68, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methyloceanibacter stevinii", "strain": "strain=R-67176", "accession": "GCA_001723355.1", "taxid": 1774970, "species_taxid": 1774970, "relation_to_type": "type", "validated": true, "ani": 76.3325, "matched_fragments": 79, "total_fragments": 955, "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": 76.2887, "matched_fragments": 106, "total_fragments": 955, "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": 76.2452, "matched_fragments": 155, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanicella actignis", "strain": "strain=DSM 22673", "accession": "GCA_008124525.1", "taxid": 1189325, "species_taxid": 1189325, "relation_to_type": "type", "validated": true, "ani": 76.2236, "matched_fragments": 135, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oricola indica", "strain": "strain=JL-62", "accession": "GCA_019966595.1", "taxid": 2872591, "species_taxid": 2872591, "relation_to_type": "type", "validated": true, "ani": 76.1489, "matched_fragments": 104, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 76.1331, "matched_fragments": 128, "total_fragments": 955, "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": 76.1248, "matched_fragments": 140, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chelatococcus asaccharovorans", "strain": "strain=DSM 6462", "accession": "GCA_018398275.1", "taxid": 28210, "species_taxid": 28210, "relation_to_type": "type", "validated": true, "ani": 76.0867, "matched_fragments": 113, "total_fragments": 955, "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": 76.0866, "matched_fragments": 113, "total_fragments": 955, "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": 76.0646, "matched_fragments": 123, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodopseudomonas pentothenatexigens", "strain": "strain=JA575", "accession": "GCA_003385925.1", "taxid": 999699, "species_taxid": 999699, "relation_to_type": "type", "validated": true, "ani": 76.0519, "matched_fragments": 139, "total_fragments": 955, "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": 76.0519, "matched_fragments": 139, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neomegalonema perideroedes", "strain": "strain=DSM 15528", "accession": "GCA_000374145.1", "taxid": 217219, "species_taxid": 217219, "relation_to_type": "type", "validated": true, "ani": 76.047, "matched_fragments": 76, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella kummerowiae", "strain": "strain=CCBAU 25048", "accession": "GCA_009827055.1", "taxid": 417745, "species_taxid": 417745, "relation_to_type": "type", "validated": true, "ani": 75.9597, "matched_fragments": 96, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium terrae", "strain": "strain=17Sr1-28", "accession": "GCA_003173755.1", "taxid": 2202827, "species_taxid": 2202827, "relation_to_type": "type", "validated": true, "ani": 75.8531, "matched_fragments": 135, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Celeribacter neptunius", "strain": "strain=DSM 26471", "accession": "GCA_900113955.1", "taxid": 588602, "species_taxid": 588602, "relation_to_type": "type", "validated": true, "ani": 75.8137, "matched_fragments": 75, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseococcus pinisoli", "strain": "strain=XZZS9", "accession": "GCA_018413645.1", "taxid": 2835040, "species_taxid": 2835040, "relation_to_type": "type", "validated": true, "ani": 75.8121, "matched_fragments": 74, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovastum atsumiense", "strain": "strain=G2-11", "accession": "GCA_937425535.1", "taxid": 504468, "species_taxid": 504468, "relation_to_type": "type", "validated": true, "ani": 75.8054, "matched_fragments": 146, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovarius lipocyclicus", "strain": "strain=CCUG 44693", "accession": "GCA_009900765.1", "taxid": 268410, "species_taxid": 268410, "relation_to_type": "type", "validated": true, "ani": 75.7581, "matched_fragments": 108, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella yambaruensis", "strain": "strain=DSM 18801", "accession": "GCA_022899355.1", "taxid": 415996, "species_taxid": 415996, "relation_to_type": "type", "validated": true, "ani": 75.7519, "matched_fragments": 143, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cohaesibacter intestini", "strain": "strain=YE-B6", "accession": "GCA_003324485.1", "taxid": 2211145, "species_taxid": 2211145, "relation_to_type": "type", "validated": true, "ani": 75.6325, "matched_fragments": 76, "total_fragments": 955, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.46, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCA_002869085.1", "gtdb_species": "s__BM303 sp002869085", "ani": 100.0, "matched_fragments": 940, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__BM303;g__BM303", "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": "conclusive" }, { "accession": "GCF_013341275.1", "gtdb_species": "s__Methyloligella sp013341275", "ani": 77.1531, "matched_fragments": 149, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella", "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_003576695.1", "gtdb_species": "s__Nordella sp003576695", "ani": 76.9454, "matched_fragments": 146, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella", "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_000739695.1", "gtdb_species": "s__Tepidicaulis marinus", "ani": 76.84, "matched_fragments": 122, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Tepidicaulis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", 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76.5346, "matched_fragments": 151, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella", "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_900156025.1", "gtdb_species": "s__Bosea sp900156025", "ani": 76.5068, "matched_fragments": 127, "total_fragments": 955, "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_001938945.1", "gtdb_species": "s__Pararhizobium rhizosphaerae", "ani": 76.5019, "matched_fragments": 143, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001723295.1", "gtdb_species": "s__Methyloceanibacter marginalis", "ani": 76.4658, "matched_fragments": 74, "total_fragments": 955, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter", "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_002304505.1", "gtdb_species": "s__NCEH01 sp002304505", "ani": 76.4563, "matched_fragments": 127, "total_fragments": 955, 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