{ "type": "genome", "identifier": "GCA_004293855.1", "organism": "Oscillatoriales cyanobacterium", "title": "Oscillatoriales cyanobacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "Jill Banfield's Lab at Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004293855.1", "bioproject": "PRJNA448579", "biosample": "SAMN10167068", "wgs_master": "RDYZ00000000.1", "refseq_category": "na", "taxid": "1151", "species_taxid": "1151", "organism_name": "Oscillatoriales cyanobacterium", "infraspecific_name": "", "isolate": "PH2015_06S_54_30", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/22", "asm_name": "ASM429385v1", "submitter": "Jill Banfield's Lab at Berkeley", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/293/855/GCA_004293855.1_ASM429385v1", "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": "2019-02-22", "dateModified": "2019-02-22", "datePublished": "2019-02-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Oscillatoriales cyanobacterium" ], "sample_taxid": [ "1151" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: California, Eel River, South Fork Eel River between Leggett and Piercy" ], "sample_host_location_id": [], "data_size": "1.011 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 90.74, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3523472", "Number of Sequences": "496", "Longest Sequences (bp)": "42909", "N50 (bp)": "10963", "Gap Ratio (%)": "0.003604", "GCcontent (%)": "53.6", "Number of CDSs": "2445", "Average Protein Length": "320.6", "Coding Ratio (%)": "66.7", "Number of rRNAs": "1", "Number of tRNAs": "33", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [], "cc_result": { "completeness": 90.74, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004293855.1", "gtdb_species": "s__RDYZ01 sp004293855", "ani": 100.0, "matched_fragments": 915, "total_fragments": 921, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__RDYZ01", "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": "GCA_012033105.1", "gtdb_species": "s__RDYZ01 sp012033105", "ani": 83.0343, "matched_fragments": 662, "total_fragments": 921, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__RDYZ01", "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_011390275.1", "gtdb_species": "s__RDYZ01 sp011390275", "ani": 82.8815, "matched_fragments": 729, "total_fragments": 921, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__RDYZ01", "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": "-" }, { 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"s__DVED01 sp003695795", "ani": 75.3681, "matched_fragments": 51, "total_fragments": 921, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__DVED01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.397, "cell_length": 0.602, "doubling_h": 1.2, "growth_tmp": 21.7, "optimum_tmp": 27.0, "optimum_ph": 9.5, "genome_size": 5876746.851, "gc_content": 42.975, "coding_genes": 6233.5, "rRNA16S_genes": 3.0, "tRNA_genes": 60.0, "gram_stain": 0.111, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.333, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.666, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.8, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.2 }, "_gtdb_taxon": [ "d__Bacteria", "p__Cyanobacteriota", "c__Cyanobacteriia", "o__Cyanobacteriales", "f__Geitlerinemaceae", "g__RDYZ01", "s__RDYZ01 sp004293855" ], "_genome_taxon": [ "Oscillatoriales", "cyanobacterium", "d__Bacteria", "p__Cyanobacteriota", "c__Cyanobacteriia", "o__Cyanobacteriales", "f__Geitlerinemaceae", "g__RDYZ01", "s__RDYZ01 sp004293855", "Bacteria", "Cyanobacteriota", "Cyanobacteriia", "Cyanobacteriales", "Geitlerinemaceae", "RDYZ01", "RDYZ01", "sp004293855" ], "_meo": [ { "id": "MEO_0000116", "label": "biofilm" }, { "id": "MEO_0000082", "label": "river" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }