{ "type": "genome", "identifier": "GCA_010026045.1", "organism": "Alphaproteobacteria bacterium", "title": "Alphaproteobacteria bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Georgia Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCA_010026045.1", "bioproject": "PRJNA495371", "biosample": "SAMN10223493", "wgs_master": "RGPW00000000.1", "refseq_category": "na", "taxid": "1913988", "species_taxid": "1913988", "organism_name": "Alphaproteobacteria bacterium", "infraspecific_name": "", "isolate": "WB8_3_147", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/31", "asm_name": "ASM1002604v1", "submitter": "Georgia Institute of Technology", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/026/045/GCA_010026045.1_ASM1002604v1", "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": "2020-01-31", "dateModified": "2020-01-31", "datePublished": "2020-01-31", "_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: Chattahoochee River" ], "sample_host_location_id": [], "data_size": "0.839 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 13.0, "max": 13.0 }, "completeness": 74.59, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2941489", "Number of Sequences": "695", "Longest Sequences (bp)": "33599", "N50 (bp)": "5730", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.0", "Number of CDSs": "2298", "Average Protein Length": "284.6", "Coding Ratio (%)": "66.7", "Number of rRNAs": "0", "Number of tRNAs": "33", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Methylosinus sporium", "strain": "strain=DSM 17706", "accession": "GCA_009811675.1", "taxid": 428, "species_taxid": 428, "relation_to_type": "type", "validated": true, "ani": 76.44, "matched_fragments": 53, "total_fragments": 623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylosinus sporium", "strain": "strain=DSM 17706", "accession": "GCA_003113265.1", "taxid": 428, "species_taxid": 428, "relation_to_type": "type", "validated": true, "ani": 76.4318, "matched_fragments": 52, "total_fragments": 623, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 74.59, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903903935.1", "gtdb_species": "s__28-YEA-48 sp903903935", "ani": 90.1985, "matched_fragments": 358, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "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_900299065.1", "gtdb_species": "s__28-YEA-48 sp900299065", "ani": 81.8349, "matched_fragments": 356, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "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_903851305.1", "gtdb_species": "s__28-YEA-48 sp903851305", "ani": 76.8828, "matched_fragments": 75, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.92", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_903902915.1", "gtdb_species": "s__28-YEA-48 sp903902915", "ani": 76.521, "matched_fragments": 71, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_001898965.1", "gtdb_species": "s__28-YEA-48 sp001898965", "ani": 76.1188, "matched_fragments": 55, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "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": "GCF_900104955.1", "gtdb_species": "s__28-YEA-48 sp900104955", "ani": 76.088, "matched_fragments": 50, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "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_903897875.1", "gtdb_species": "s__28-YEA-48 sp903897875", "ani": 75.6393, "matched_fragments": 54, "total_fragments": 623, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Beijerinckiaceae", "g__28-YEA-48", "s__" ], "_genome_taxon": [ "Alphaproteobacteria", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Beijerinckiaceae", "g__28-YEA-48", "s__", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Beijerinckiaceae", "28-YEA-48", "s", "", "" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }