{ "type": "genome", "identifier": "GCA_020048835.1", "organism": "Planktothrix sp. bin_235_243", "title": "Planktothrix sp. bin_235_243", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Michigan", "publication": [ {} ], "properties": { "assembly_accession": "GCA_020048835.1", "bioproject": "PRJNA72255", "biosample": "SAMN20441948", "wgs_master": "JAIFLY000000000.1", "refseq_category": "na", "taxid": "2856834", "species_taxid": "2856834", "organism_name": "Planktothrix sp. bin_235_243", "infraspecific_name": "", "isolate": "bin_235_243", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/09/20", "asm_name": "ASM2004883v1", "submitter": "University of Michigan", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/048/835/GCA_020048835.1_ASM2004883v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-09-20", "dateModified": "2021-09-20", "datePublished": "2021-09-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Planktothrix sp. bin_235_243" ], "sample_taxid": [ "2856834" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: northwestern Lake Huron" ], "sample_host_location_id": [], "data_size": "1.624 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 81.1, "contamination": 35.94, "strain_heterogeneity": 29.17, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "5709010", "Number of Sequences": "1194", "Longest Sequences (bp)": "47235", "N50 (bp)": "6268", "Gap Ratio (%)": "0.014048", "GCcontent (%)": "40.1", "Number of CDSs": "4435", "Average Protein Length": "270.5", "Coding Ratio (%)": "63.1", "Number of rRNAs": "0", "Number of tRNAs": "46", "Number of CRISPRs": "11" }, "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": 88.4859, "matched_fragments": 754, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Planktothrix tepida", "strain": "strain=PCC9214", "accession": "GCA_904830955.1", "taxid": 1678309, "species_taxid": 1678309, "relation_to_type": "type", "validated": true, "ani": 83.0361, "matched_fragments": 775, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nostoc favosum", "strain": "strain=CHAB 5714", "accession": "GCA_020829495.1", "taxid": 2907819, "species_taxid": 2907819, "relation_to_type": "type", "validated": true, "ani": 75.533, "matched_fragments": 71, "total_fragments": 1248, "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": 75.4243, "matched_fragments": 67, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gloeothece citriformis", "strain": "strain=PCC 7424", "accession": "GCA_000021825.1", "taxid": 2546356, "species_taxid": 2546356, "relation_to_type": "type", "validated": true, "ani": 75.3676, "matched_fragments": 86, "total_fragments": 1248, "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": 75.3377, "matched_fragments": 89, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Allocoleopsis franciscana", "strain": "strain=PCC 7113", "accession": "GCA_000317515.1", "taxid": 2886352, "species_taxid": 2886352, "relation_to_type": "type", "validated": true, "ani": 75.2611, "matched_fragments": 61, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crocosphaera watsonii", "strain": "strain=WH 8501", "accession": "GCA_000167195.1", "taxid": 263511, "species_taxid": 263511, "relation_to_type": "suspected-type", "validated": true, "ani": 75.2435, "matched_fragments": 63, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dulcicalothrix desertica", "strain": "strain=PCC 7102", "accession": "GCA_003991905.1", "taxid": 32056, "species_taxid": 32056, "relation_to_type": "type", "validated": true, "ani": 75.0103, "matched_fragments": 51, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dulcicalothrix desertica", "strain": "strain=PCC 7102", "accession": "GCA_007830875.1", "taxid": 32056, "species_taxid": 32056, "relation_to_type": "type", "validated": true, "ani": 74.9726, "matched_fragments": 50, "total_fragments": 1248, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 81.1, "contamination": 35.94, "strain_heterogeneity": 29.17 }, "gtdb_result": [ { "accession": "GCA_003456035.1", "gtdb_species": "s__Planktothrix sp003456035", "ani": 98.3885, "matched_fragments": 711, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "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": "GCF_900009275.2", "gtdb_species": "s__Planktothrix rubescens", "ani": 88.8645, "matched_fragments": 808, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "ani_circumscription_radius": 96.6657, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "97.64", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_003609755.1", "gtdb_species": "s__Planktothrix agardhii", "ani": 88.4734, "matched_fragments": 755, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "ani_circumscription_radius": 96.6657, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900009135.1", "gtdb_species": "s__Planktothrix sp900009135", "ani": 88.2928, "matched_fragments": 825, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "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_001873365.1", "gtdb_species": "s__Planktothrix sp001873365", "ani": 87.9502, "matched_fragments": 772, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "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_900009265.2", "gtdb_species": "s__Planktothrix paucivesiculata", "ani": 87.6209, "matched_fragments": 785, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "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_903893625.1", "gtdb_species": "s__Planktothrix sp903893625", "ani": 85.9706, "matched_fragments": 773, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "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_900010725.2", "gtdb_species": "s__Planktothrix serta", "ani": 85.2406, "matched_fragments": 803, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix", "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_001698425.1", "gtdb_species": "s__Kamptonema sp001698425", "ani": 81.8169, "matched_fragments": 288, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Kamptonema", "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_000332155.1", "gtdb_species": "s__Kamptonema formosum", "ani": 79.022, "matched_fragments": 238, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Kamptonema", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003542015.1", "gtdb_species": "s__Microcoleus sp003542015", "ani": 78.6225, "matched_fragments": 194, "total_fragments": 1248, "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_013299165.1", "gtdb_species": "s__Microcoleus sp013299165", "ani": 77.4486, "matched_fragments": 148, "total_fragments": 1248, "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_004292955.1", "gtdb_species": "s__Microcoleus sp004292955", "ani": 77.3689, "matched_fragments": 170, "total_fragments": 1248, "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": "GCF_002368075.1", "gtdb_species": "s__Sphaerospermopsis kisseleviana_A", "ani": 75.3426, "matched_fragments": 102, "total_fragments": 1248, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Sphaerospermopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.397, "cell_length": 0.602, "doubling_h": 1.2, "growth_tmp": 21.1, "optimum_tmp": 20.0, "optimum_ph": null, "genome_size": 5371882.0, "gc_content": 39.282, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.5, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.5, "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": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Cyanobacteriota", "c__Cyanobacteriia", "o__Cyanobacteriales", "f__Microcoleaceae", "g__Planktothrix", "s__Planktothrix sp003456035" ], "_genome_taxon": [ "Planktothrix", "sp.", "bin_235_243", "d__Bacteria", "p__Cyanobacteriota", "c__Cyanobacteriia", "o__Cyanobacteriales", "f__Microcoleaceae", "g__Planktothrix", "s__Planktothrix sp003456035", "Bacteria", "Cyanobacteriota", "Cyanobacteriia", "Cyanobacteriales", "Microcoleaceae", "Planktothrix", "Planktothrix", "sp003456035" ], "_meo": [ { "id": "MEO_0000116", "label": "biofilm" }, { "id": "MEO_0000038", "label": "freshwater" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }