{ "type": "genome", "identifier": "GCF_000317615.1", "organism": "Dactylococcopsis salina PCC 8305", "title": "Dactylococcopsis salina PCC 8305", "description": "na", "data type": "Genome sequencing and assembly", "organization": "JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000317615.1", "bioproject": "PRJNA224116", "biosample": "SAMN02261331", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "13035", "species_taxid": "292566", "organism_name": "Dactylococcopsis salina PCC 8305", "infraspecific_name": "strain=PCC 8305", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/12/07", "asm_name": "ASM31761v1", "asm_submitter": "JGI", "gbrs_paired_asm": "GCA_000317615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/317/615/GCF_000317615.1_ASM31761v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3781008", "genome_size_ungapped": "3781008", "gc_percent": "42.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000317615.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "3830", "protein_coding_gene_count": "3721", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-12-07", "dateModified": "2012-12-07", "datePublished": "2012-12-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Dactylococcopsis salina PCC 8305" ], "sample_taxid": [ "13035" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [ "None" ], "sample_host_disease_id": [], "sample_host_location": [ "Israel" ], "sample_host_location_id": [], "data_size": "1.042 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3781008", "Number of Sequences": "1", "Longest Sequences (bp)": "3781008", "N50 (bp)": "3781008", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.4", "Number of CDSs": "3488", "Average Protein Length": "298.5", "Coding Ratio (%)": "82.6", "Number of rRNAs": "6", "Number of tRNAs": "43", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Dactylococcopsis salina", "strain": "strain=PCC 8305", "accession": "GCA_000317615.1", "taxid": 292566, "species_taxid": 292566, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1260, "total_fragments": 1260, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Euhalothece natronophila", "strain": "strain=Z-M001", "accession": "GCA_007904085.1", "taxid": 577489, "species_taxid": 577489, "relation_to_type": "type", "validated": true, "ani": 78.3159, "matched_fragments": 448, "total_fragments": 1260, "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": 76.3179, "matched_fragments": 57, "total_fragments": 1260, "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": 76.2674, "matched_fragments": 83, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oscillatoria acuminata", "strain": "strain=PCC 6304", "accession": "GCA_000317105.1", "taxid": 118323, "species_taxid": 118323, "relation_to_type": "type", "validated": true, "ani": 76.1251, "matched_fragments": 56, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Crocosphaera chwakensis", "strain": "strain=CCY0110", "accession": "GCA_000169335.1", "taxid": 2546361, "species_taxid": 2546361, "relation_to_type": "type", "validated": true, "ani": 76.042, "matched_fragments": 80, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rippkaea orientalis", "strain": "strain=PCC 8801", "accession": "GCA_000021805.1", "taxid": 2546366, "species_taxid": 2546366, "relation_to_type": "type", "validated": true, "ani": 75.9822, "matched_fragments": 88, "total_fragments": 1260, "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": 75.8875, "matched_fragments": 64, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000317615.1", "gtdb_species": "s__Halothece salina", "ani": 100.0, "matched_fragments": 1260, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece", "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_000317635.1", "gtdb_species": "s__Halothece sp000317635", "ani": 79.5842, "matched_fragments": 578, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece", "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_009909085.1", "gtdb_species": "s__Halothece sp009909085", "ani": 78.4823, "matched_fragments": 463, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece", "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_007904085.1", "gtdb_species": "s__Halothece natronophila", "ani": 78.3824, "matched_fragments": 446, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece", "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_003021905.1", "gtdb_species": "s__Halothece sp003021905", "ani": 76.9195, "matched_fragments": 325, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece", "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_900009135.1", "gtdb_species": "s__Planktothrix sp900009135", "ani": 76.6742, "matched_fragments": 52, "total_fragments": 1260, "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_018610095.1", "gtdb_species": "s__Halothece sp018610095", "ani": 76.6295, "matched_fragments": 236, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece", "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_000021825.1", "gtdb_species": "s__Gloeothece citriformis", "ani": 76.4094, "matched_fragments": 82, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae;g__Gloeothece", "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_000314005.1", "gtdb_species": "s__Spirulina_A subsalsa", "ani": 76.175, "matched_fragments": 72, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina_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_000317105.1", "gtdb_species": "s__Oscillatoria acuminata", "ani": 75.981, "matched_fragments": 53, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oscillatoria", "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_000169335.1", "gtdb_species": "s__Crocosphaera chwakensis", "ani": 75.8712, "matched_fragments": 76, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera", "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_004323185.1", "gtdb_species": "s__Fischerella prolifica", "ani": 75.5183, "matched_fragments": 53, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "96.24", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014697625.1", "gtdb_species": "s__Trichormus azotica", "ani": 75.2251, "matched_fragments": 56, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus", "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 }, "_genome_taxon": [ "Dactylococcopsis", "salina", "PCC", "8305" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }