{ "type": "genome", "identifier": "GCA_004292585.1", "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_004292585.1", "bioproject": "PRJNA448579", "biosample": "SAMN10167114", "wgs_master": "RDXF00000000.1", "refseq_category": "na", "taxid": "1151", "species_taxid": "1151", "organism_name": "Oscillatoriales cyanobacterium", "infraspecific_name": "", "isolate": "PH2015_13U_45_97", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/22", "asm_name": "ASM429258v1", "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/004/292/585/GCA_004292585.1_ASM429258v1", "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, Larabee Creek near mouth" ], "sample_host_location_id": [], "data_size": "1.581 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.46, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "5548356", "Number of Sequences": "524", "Longest Sequences (bp)": "82343", "N50 (bp)": "17456", "Gap Ratio (%)": "0.001910", "GCcontent (%)": "44.7", "Number of CDSs": "4276", "Average Protein Length": "312.1", "Coding Ratio (%)": "72.2", "Number of rRNAs": "1", "Number of tRNAs": "42", "Number of CRISPRs": "8" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Planktothrix agardhii", "strain": "strain=NIES-204", "accession": "GCA_003609755.1", "taxid": 1160, "species_taxid": 1160, "relation_to_type": "type", "validated": true, "ani": 76.1017, "matched_fragments": 88, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Argonema galeatum", "strain": "strain=A003/A1", "accession": "GCA_023333595.1", "taxid": 2942762, "species_taxid": 2942762, "relation_to_type": "type", "validated": true, "ani": 76.0633, "matched_fragments": 181, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Argonema antarcticum", "strain": "strain=A004/B2", "accession": "GCA_023333585.1", "taxid": 2942763, "species_taxid": 2942763, "relation_to_type": "type", "validated": true, "ani": 76.0033, "matched_fragments": 177, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anabaena cylindrica", "strain": "strain=NIES-19", "accession": "GCA_002367955.1", "taxid": 1165, "species_taxid": 1165, "relation_to_type": "type", "validated": true, "ani": 75.9958, "matched_fragments": 85, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Anabaena cylindrica", "strain": "strain=PCC 7122", "accession": "GCA_000317695.1", "taxid": 1165, "species_taxid": 1165, "relation_to_type": "type", "validated": true, "ani": 75.9919, "matched_fragments": 82, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Moorena producens", "strain": "strain=3L", "accession": "GCA_001942475.1", "taxid": 1155739, "species_taxid": 1155739, "relation_to_type": "type", "validated": true, "ani": 75.7636, "matched_fragments": 65, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nostoc punctiforme", "strain": "strain=ATCC 29133; PCC 73102", "accession": "GCA_000020025.1", "taxid": 272131, "species_taxid": 272131, "relation_to_type": "type", "validated": true, "ani": 75.7468, "matched_fragments": 100, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Moorena producens", "strain": "strain=3L", "accession": "GCA_000211815.1", "taxid": 1155739, "species_taxid": 1155739, "relation_to_type": "type", "validated": true, "ani": 75.7391, "matched_fragments": 67, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Iningainema tapete", "strain": "strain=BLCC-T55", "accession": "GCA_014698965.1", "taxid": 2806730, "species_taxid": 2806730, "relation_to_type": "type", "validated": true, "ani": 75.6, "matched_fragments": 100, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chlorogloeopsis fritschii", "strain": "strain=PCC 6912", "accession": "GCA_003990575.1", "taxid": 1124, "species_taxid": 1124, "relation_to_type": "type", "validated": true, "ani": 75.4553, "matched_fragments": 67, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Okeania hirsuta", "strain": "strain=PAB10Feb10-1", "accession": "GCA_003838195.1", "taxid": 1458930, "species_taxid": 1458930, "relation_to_type": "type", "validated": true, "ani": 75.2522, "matched_fragments": 63, "total_fragments": 1579, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.46, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004292745.1", "gtdb_species": "s__Microcoleus sp004292745", "ani": 99.7916, "matched_fragments": 1485, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "99.38", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_002412335.2", "gtdb_species": "s__Microcoleus bourrellyi", "ani": 87.2654, "matched_fragments": 1077, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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_004294385.1", "gtdb_species": "s__Microcoleus sp004294385", "ani": 87.0583, "matched_fragments": 1229, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003542015.1", "gtdb_species": "s__Microcoleus sp003542015", "ani": 86.3856, "matched_fragments": 1013, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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_014695295.1", "gtdb_species": "s__Microcoleus sp014695295", "ani": 83.1653, "matched_fragments": 1188, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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_000317475.1", "gtdb_species": "s__Microcoleus sp000317475", "ani": 83.151, "matched_fragments": 1270, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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_003003725.1", "gtdb_species": "s__Microcoleus sp003003725", "ani": 83.1068, "matched_fragments": 1097, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013179805.1", "gtdb_species": "s__Microcoleus asticus", "ani": 83.0259, "matched_fragments": 1213, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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_014695175.1", "gtdb_species": "s__Microcoleus sp014695175", "ani": 82.9906, "matched_fragments": 1137, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.46", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_004292955.1", "gtdb_species": "s__Microcoleus sp004292955", "ani": 82.9407, "matched_fragments": 1206, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "98.79", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCA_012035135.1", "gtdb_species": "s__Microcoleus sp012035135", "ani": 82.9158, "matched_fragments": 991, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000214075.1", "gtdb_species": "s__Microcoleus vaginatus", "ani": 82.8991, "matched_fragments": 1197, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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_013299185.1", "gtdb_species": "s__Microcoleus sp013299185", "ani": 82.5542, "matched_fragments": 1237, "total_fragments": 1579, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus", "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": 0.397, "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__Microcoleaceae", "g__Microcoleus", "s__Microcoleus sp004292745" ], "_genome_taxon": [ "Oscillatoriales", "cyanobacterium", "d__Bacteria", "p__Cyanobacteriota", "c__Cyanobacteriia", "o__Cyanobacteriales", "f__Microcoleaceae", "g__Microcoleus", "s__Microcoleus sp004292745", "Bacteria", "Cyanobacteriota", "Cyanobacteriia", "Cyanobacteriales", "Microcoleaceae", "Microcoleus", "Microcoleus", "sp004292745" ], "_meo": [ { "id": "MEO_0000116", "label": "biofilm" }, { "id": "MEO_0000082", "label": "river" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }