{ "type": "genome", "identifier": "GCA_001603295.1", "organism": "Rhodobacterales bacterium Alpha_02", "title": "Rhodobacterales bacterium Alpha_02", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of Queensland", "publication": [ {} ], "properties": { "assembly_accession": "GCA_001603295.1", "bioproject": "PRJNA284316", "biosample": "SAMN03837493", "wgs_master": "LUYO00000000.1", "refseq_category": "na", "taxid": "1674811", "species_taxid": "1674811", "organism_name": "Rhodobacterales bacterium Alpha_02", "infraspecific_name": "", "isolate": "Alpha_02", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/03/30", "asm_name": "ASM160329v1", "submitter": "University of Queensland", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/603/295/GCA_001603295.1_ASM160329v1", "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": "2016-03-30", "dateModified": "2016-03-30", "datePublished": "2016-03-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodobacterales bacterium Alpha_02" ], "sample_taxid": [ "1674811" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia" ], "sample_host_location_id": [], "data_size": "0.969 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3555386", "Number of Sequences": "259", "Longest Sequences (bp)": "75366", "N50 (bp)": "23837", "Gap Ratio (%)": "0.014485", "GCcontent (%)": "67.7", "Number of CDSs": "3050", "Average Protein Length": "318.0", "Coding Ratio (%)": "81.8", "Number of rRNAs": "1", "Number of tRNAs": "36", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pleomorphomonas koreensis", "strain": "strain=DSM 23070", "accession": "GCA_000425185.1", "taxid": 257440, "species_taxid": 257440, "relation_to_type": "type", "validated": true, "ani": 95.0142, "matched_fragments": 928, "total_fragments": 1052, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pleomorphomonas carboxyditropha", "strain": "strain=SVCO-16", "accession": "GCA_002770725.1", "taxid": 2023338, "species_taxid": 2023338, "relation_to_type": "type", "validated": true, "ani": 88.7689, "matched_fragments": 871, "total_fragments": 1052, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pleomorphomonas diazotrophica", "strain": "strain=R5-392", "accession": "GCA_002844595.1", "taxid": 1166257, "species_taxid": 1166257, "relation_to_type": "type", "validated": true, "ani": 86.2249, "matched_fragments": 789, "total_fragments": 1052, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pleomorphomonas diazotrophica", "strain": "strain=R5-392", "accession": "GCA_900114935.1", "taxid": 1166257, "species_taxid": 1166257, "relation_to_type": "type", "validated": true, "ani": 86.139, "matched_fragments": 801, "total_fragments": 1052, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pleomorphomonas oryzae", "strain": "strain=DSM 16300", "accession": "GCA_000422965.1", "taxid": 261934, "species_taxid": 261934, "relation_to_type": "type", "validated": true, "ani": 84.7896, "matched_fragments": 800, "total_fragments": 1052, "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": 77.9105, "matched_fragments": 354, "total_fragments": 1052, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jiella sonneratiae", "strain": "strain=MQZ13P-4", "accession": "GCA_017353515.1", "taxid": 2816856, "species_taxid": 2816856, "relation_to_type": "type", "validated": true, "ani": 77.7282, "matched_fragments": 332, "total_fragments": 1052, "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": 76.9919, "matched_fragments": 366, "total_fragments": 1052, "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": 76.9545, "matched_fragments": 371, "total_fragments": 1052, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium nonmethylotrophicum", "strain": "strain=6HR-1", "accession": "GCA_004745635.1", "taxid": 1141884, "species_taxid": 1141884, "relation_to_type": "type", "validated": true, "ani": 76.7961, "matched_fragments": 368, "total_fragments": 1052, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000425185.1", "gtdb_species": "s__Pleomorphomonas koreensis", "ani": 95.0362, "matched_fragments": 927, "total_fragments": 1052, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.03", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002770725.1", "gtdb_species": "s__Pleomorphomonas carboxyditropha", "ani": 88.7601, "matched_fragments": 872, "total_fragments": 1052, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.10", "min_intra_species_ani": "98.10", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002844595.1", "gtdb_species": "s__Pleomorphomonas diazotrophica", "ani": 86.1885, "matched_fragments": 792, "total_fragments": 1052, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_011759535.1", "gtdb_species": "s__Pleomorphomonas sp011759535", "ani": 84.7735, "matched_fragments": 787, "total_fragments": 1052, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018262505.1", "gtdb_species": "s__Pleomorphomonas sp018262505", "ani": 84.6223, "matched_fragments": 732, "total_fragments": 1052, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.197, "cell_length": 0.193, "doubling_h": 0.42, "growth_tmp": 28.265, "optimum_tmp": 28.878, "optimum_ph": 7.446, "genome_size": 4160747.54, "gc_content": 62.69, "coding_genes": 4005.416, "rRNA16S_genes": 2.751, "tRNA_genes": 48.894, "gram_stain": 0.003, "sporulation": 0.014, "motility": 0.422, "range_salinity": 0.916, "facultative_respiration": 0.083, "anaerobic_respiration": 0.046, "aerobic_respiration": 0.869, "mesophilic_range_tmp": 0.928, "thermophilic_range_tmp": 0.035, "psychrophilic_range_tmp": 0.035, "bacillus_cell_shape": 0.849, "coccus_cell_shape": 0.042, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.107, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Pleomorphomonadaceae", "g__Pleomorphomonas", "s__Pleomorphomonas sp001603295" ], "_genome_taxon": [ "Rhodobacterales", "bacterium", "Alpha_02", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Pleomorphomonadaceae", "g__Pleomorphomonas", "s__Pleomorphomonas sp001603295", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Pleomorphomonadaceae", "Pleomorphomonas", "Pleomorphomonas", "sp001603295" ], "_meo": [ { "id": "MEO_0001192", "label": "anaerobic digester" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }