{ "type": "genome", "identifier": "GCA_004356855.1", "organism": "Alphaproteobacteria bacterium", "title": "Alphaproteobacteria bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Scripps Institution of Oceanography", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004356855.1", "bioproject": "PRJNA526329", "biosample": "SAMN11097086", "wgs_master": "SMXT00000000.1", "refseq_category": "na", "taxid": "1913988", "species_taxid": "1913988", "organism_name": "Alphaproteobacteria bacterium", "infraspecific_name": "", "isolate": "N074bin41", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/19", "asm_name": "ASM435685v1", "submitter": "Scripps Institution of Oceanography", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/356/855/GCA_004356855.1_ASM435685v1", "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": "2019-03-19", "dateModified": "2019-03-19", "datePublished": "2019-03-19", "_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": [ "Pacific Ocean" ], "sample_host_location_id": [], "data_size": "0.563 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 87.5, "contamination": 19.13, "strain_heterogeneity": 7.14, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2011275", "Number of Sequences": "213", "Longest Sequences (bp)": "27184", "N50 (bp)": "10066", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.8", "Number of CDSs": "1735", "Average Protein Length": "313.5", "Coding Ratio (%)": "81.1", "Number of rRNAs": "0", "Number of tRNAs": "21", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Afifella pfennigii", "strain": "strain=DSM 17143", "accession": "GCA_000688515.1", "taxid": 209897, "species_taxid": 209897, "relation_to_type": "type", "validated": true, "ani": 77.572, "matched_fragments": 171, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afifella marina", "strain": "strain=DSM 2698", "accession": "GCA_900102695.1", "taxid": 1080, "species_taxid": 1080, "relation_to_type": "type", "validated": true, "ani": 77.308, "matched_fragments": 82, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afifella marina", "strain": "strain=DSM 2698", "accession": "GCA_003258905.1", "taxid": 1080, "species_taxid": 1080, "relation_to_type": "type", "validated": true, "ani": 77.2897, "matched_fragments": 84, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afifella marina", "strain": "strain=DSM 2698", "accession": "GCA_016584015.1", "taxid": 1080, "species_taxid": 1080, "relation_to_type": "type", "validated": true, "ani": 77.2234, "matched_fragments": 86, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Afifella aestuarii", "strain": "strain=JA968", "accession": "GCA_004023665.1", "taxid": 1909496, "species_taxid": 1909496, "relation_to_type": "type", "validated": true, "ani": 77.1581, "matched_fragments": 94, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Propylenella binzhouense", "strain": "strain=L72", "accession": "GCA_009866965.1", "taxid": 2555902, "species_taxid": 2555902, "relation_to_type": "type", "validated": true, "ani": 76.955, "matched_fragments": 110, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium muleiense", "strain": "strain=CGMCC 1.11022", "accession": "GCA_900099905.1", "taxid": 1004279, "species_taxid": 1004279, "relation_to_type": "type", "validated": true, "ani": 76.698, "matched_fragments": 115, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium metallidurans", "strain": "strain=STM 2683", "accession": "GCA_000350085.1", "taxid": 489722, "species_taxid": 489722, "relation_to_type": "type", "validated": true, "ani": 76.6285, "matched_fragments": 108, "total_fragments": 549, "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": 76.5245, "matched_fragments": 67, "total_fragments": 549, "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": 76.5215, "matched_fragments": 99, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium temperatum", "strain": "strain=SDW018", "accession": "GCA_002284575.1", "taxid": 241416, "species_taxid": 241416, "relation_to_type": "type", "validated": true, "ani": 76.4792, "matched_fragments": 111, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mesorhizobium opportunistum", "strain": "strain=WSM2075", "accession": "GCA_000176035.2", "taxid": 593909, "species_taxid": 593909, "relation_to_type": "type", "validated": true, "ani": 76.4785, "matched_fragments": 111, "total_fragments": 549, "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": 76.4664, "matched_fragments": 69, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stappia taiwanensis", "strain": "strain=DSM 23284", "accession": "GCA_013868145.1", "taxid": 992267, "species_taxid": 992267, "relation_to_type": "type", "validated": true, "ani": 76.3941, "matched_fragments": 101, "total_fragments": 549, "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": 76.3714, "matched_fragments": 90, "total_fragments": 549, "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": 76.3206, "matched_fragments": 73, "total_fragments": 549, "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": 76.305, "matched_fragments": 80, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobrevis albus", "strain": "strain=L22", "accession": "GCA_015904235.1", "taxid": 2793297, "species_taxid": 2793297, "relation_to_type": "type", "validated": true, "ani": 76.2657, "matched_fragments": 97, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium septentrionale", "strain": "strain=1S1", "accession": "GCA_011516645.4", "taxid": 1404411, "species_taxid": 1404411, "relation_to_type": "type", "validated": true, "ani": 76.2409, "matched_fragments": 80, "total_fragments": 549, "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": 76.1901, "matched_fragments": 70, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium brachiatum", "strain": "strain=B0021", "accession": "GCA_020523825.1", "taxid": 269660, "species_taxid": 269660, "relation_to_type": "type", "validated": true, "ani": 76.0574, "matched_fragments": 70, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bradyrhizobium altum", "strain": "strain=Pear77", "accession": "GCA_020889705.1", "taxid": 1571202, "species_taxid": 1571202, "relation_to_type": "type", "validated": true, "ani": 76.0267, "matched_fragments": 84, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Martelella radicis", "strain": "strain=DSM 28101", "accession": "GCA_014196625.1", "taxid": 1397476, "species_taxid": 1397476, "relation_to_type": "type", "validated": true, "ani": 75.9324, "matched_fragments": 68, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium mesophilicum", "strain": "strain=NBRC 15688", "accession": "GCA_022179445.1", "taxid": 39956, "species_taxid": 39956, "relation_to_type": "type", "validated": true, "ani": 75.91, "matched_fragments": 61, "total_fragments": 549, "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": 75.7118, "matched_fragments": 67, "total_fragments": 549, "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": 75.7118, "matched_fragments": 67, "total_fragments": 549, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 87.5, "contamination": 19.13, "strain_heterogeneity": 7.14 }, "gtdb_result": [ { "accession": "GCF_000688515.1", "gtdb_species": "s__Afifella pfennigii", "ani": 77.572, "matched_fragments": 171, "total_fragments": 549, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella", "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_900102695.1", "gtdb_species": "s__Afifella marina", "ani": 77.2876, "matched_fragments": 84, "total_fragments": 549, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella", "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": "0.99", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_004023665.1", "gtdb_species": "s__Afifella aestuarii", "ani": 77.1581, "matched_fragments": 94, "total_fragments": 549, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": 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