{ "type": "genome", "identifier": "GCA_903944355.1", "organism": "Synechococcus lacustris", "title": "Synechococcus lacustris", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "BILS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_903944355.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6945605", "wgs_master": "CAJARI000000000.1", "refseq_category": "na", "taxid": "2116544", "species_taxid": "2116544", "organism_name": "Synechococcus lacustris", "infraspecific_name": "", "isolate": "Loc090907-6m_bin-455", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/18", "asm_name": "freshwater MAG --- Loc090907-6m_bin-455", "submitter": "BILS", "gbrs_paired_asm": "GCF_903944355.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/944/355/GCA_903944355.1_freshwater_MAG_---_Loc090907-6m_bin-455", "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": "2020-07-18", "dateModified": "2020-07-18", "datePublished": "2020-07-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Synechococcus lacustris" ], "sample_taxid": [ "2116544" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Switzerland" ], "sample_host_location_id": [], "data_size": "0.691 MB", "sample_ph_range": { "min": 712.0, "max": 712.0 }, "sample_temperature_range": { "min": 128.0, "max": 128.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2475429", "Number of Sequences": "23", "Longest Sequences (bp)": "427153", "N50 (bp)": "154769", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.8", "Number of CDSs": "2517", "Average Protein Length": "295.5", "Coding Ratio (%)": "90.1", "Number of rRNAs": "0", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Synechococcus lacustris", "strain": "strain=Tous", "accession": "GCA_003011125.1", "taxid": 2116544, "species_taxid": 2116544, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3754, "matched_fragments": 207, "total_fragments": 813, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Parasynechococcus marenigrum", "strain": "strain=WH 8102", "accession": "GCA_000195975.1", "taxid": 2881428, "species_taxid": 2881428, "relation_to_type": "type", "validated": true, "ani": 77.587, "matched_fragments": 185, "total_fragments": 813, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903943975.1", "gtdb_species": "s__Synechococcus_D lacustris_A", "ani": 99.9988, "matched_fragments": 809, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.37", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.92", "num_clustered_genomes": 31, "status": "conclusive" }, { "accession": "GCF_014697415.1", "gtdb_species": "s__Cyanobium_A sp014697415", "ani": 78.9652, "matched_fragments": 326, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A", "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_003003925.1", "gtdb_species": "s__Cyanobium minutissimum", "ani": 78.8839, "matched_fragments": 341, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.57", "min_intra_species_ani": "95.57", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903871775.1", "gtdb_species": "s__CAIQIA01 sp903871775", "ani": 78.8694, "matched_fragments": 363, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__CAIQIA01", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_016463595.1", "gtdb_species": "s__BAIKAL-G1 sp016463595", "ani": 78.7274, "matched_fragments": 281, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1", "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_000316515.1", "gtdb_species": "s__Cyanobium gracile", "ani": 78.727, "matched_fragments": 320, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "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_019104765.1", "gtdb_species": "s__Vulcanococcus sp019104765", "ani": 78.623, "matched_fragments": 307, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus", "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_019038415.1", "gtdb_species": "s__Cyanobium sp019038415", "ani": 78.6102, "matched_fragments": 323, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "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_014280235.1", "gtdb_species": "s__NIES-981 sp014280235", "ani": 78.5903, "matched_fragments": 331, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.33", "min_intra_species_ani": "97.33", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016882315.1", "gtdb_species": "s__Cyanobium sp016882315", "ani": 78.5607, "matched_fragments": 335, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "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_002252675.1", "gtdb_species": "s__Cyanobium sp002252675", "ani": 78.521, "matched_fragments": 345, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "95.99", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_900088535.1", "gtdb_species": "s__NIES-981 sp900088535", "ani": 78.5199, "matched_fragments": 334, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981", "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_903855705.1", "gtdb_species": "s__BAIKAL-G1 sp903855705", "ani": 78.5194, "matched_fragments": 306, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__BAIKAL-G1", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_000708525.1", "gtdb_species": "s__Cyanobium sp000708525", "ani": 78.3869, "matched_fragments": 287, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "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_015841355.1", "gtdb_species": "s__WH-5701 sp015841355", "ani": 78.3414, "matched_fragments": 305, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701", "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_000063525.1", "gtdb_species": "s__RCC307 sp000063525", "ani": 78.3373, "matched_fragments": 300, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "97.86", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_002470305.1", "gtdb_species": "s__RCC307 sp002470305", "ani": 78.1903, "matched_fragments": 223, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__RCC307", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "97.75", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.76", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_014191755.1", "gtdb_species": "s__Cyanobium sp014191755", "ani": 78.1719, "matched_fragments": 314, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium", "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_903934375.1", "gtdb_species": "s__Vulcanococcus sp903934375", "ani": 78.1013, "matched_fragments": 276, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018623875.1", "gtdb_species": "s__Vulcanococcus sp018623875", "ani": 77.933, "matched_fragments": 150, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus", "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_014217875.1", "gtdb_species": "s__Vulcanococcus sp014217875", "ani": 77.8224, "matched_fragments": 208, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus", "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_014217855.1", "gtdb_species": "s__Synechococcus_C sp004332415", "ani": 77.6846, "matched_fragments": 173, "total_fragments": 813, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.38", "min_intra_species_ani": "96.99", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "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__Cyanobacteriota", "c__Cyanobacteriia", "o__PCC-6307", "f__Cyanobiaceae", "g__Synechococcus_D", "s__Synechococcus_D lacustris_A" ], "_genome_taxon": [ "Synechococcus", "lacustris", "d__Bacteria", "p__Cyanobacteriota", "c__Cyanobacteriia", "o__PCC-6307", "f__Cyanobiaceae", "g__Synechococcus_D", "s__Synechococcus_D lacustris_A", "Bacteria", "Cyanobacteriota", "Cyanobacteriia", "PCC-6307", "Cyanobiaceae", "Synechococcus", "D", "Synechococcus", "D", "lacustris", "A" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }