{ "type": "genome", "identifier": "GCF_900114445.1", "organism": "Salinicoccus halodurans", "title": "Salinicoccus halodurans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900114445.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216235", "wgs_master": "FOTB00000000.1", "refseq_category": "reference genome", "taxid": "407035", "species_taxid": "407035", "organism_name": "Salinicoccus halodurans", "infraspecific_name": "strain=CGMCC 1.6501", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2687453789 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900114445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/114/445/GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2735405", "genome_size_ungapped": "2734684", "gc_percent": "44.500000", "replicon_count": "0", "scaffold_count": "10", "contig_count": "10", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900114445.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2835", "protein_coding_gene_count": "2736", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Salinicoccus halodurans" ], "sample_taxid": [ "407035" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.777 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)": "2735405", "Number of Sequences": "10", "Longest Sequences (bp)": "839712", "N50 (bp)": "401895", "Gap Ratio (%)": "0.026358", "GCcontent (%)": "44.5", "Number of CDSs": "2799", "Average Protein Length": "293.2", "Coding Ratio (%)": "90.0", "Number of rRNAs": "5", "Number of tRNAs": "59", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Salinicoccus halodurans", "strain": "strain=CGMCC 1.6501", "accession": "GCA_900114445.1", 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"validated": true, "ani": 78.6747, "matched_fragments": 227, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinicoccus albus", "strain": "strain=YIM-Y21", "accession": "GCA_000385175.1", "taxid": 418756, "species_taxid": 418756, "relation_to_type": "type", "validated": true, "ani": 78.4769, "matched_fragments": 248, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinicoccus hispanicus", "strain": "strain=J-82", "accession": "GCA_009831115.1", "taxid": 157225, "species_taxid": 157225, "relation_to_type": "type", "validated": true, "ani": 78.062, "matched_fragments": 225, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Jeotgalicoccus aerolatus", "strain": "strain=CCM 7679", "accession": "GCA_014635205.1", "taxid": 709510, "species_taxid": 709510, "relation_to_type": "type", "validated": true, "ani": 77.7149, "matched_fragments": 68, 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"status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900114445.1", "gtdb_species": "s__Salinicoccus halodurans", "ani": 100.0, "matched_fragments": 905, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000986795.1", "gtdb_species": "s__Salinicoccus sediminis", "ani": 82.4924, "matched_fragments": 617, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "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_019113295.1", "gtdb_species": "s__Salinicoccus stercoripullorum", "ani": 81.9105, "matched_fragments": 545, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "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_000330705.1", "gtdb_species": "s__Salinicoccus carnicancri", "ani": 81.6846, "matched_fragments": 579, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "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_003814515.1", "gtdb_species": "s__Salinicoccus roseus", "ani": 79.1397, "matched_fragments": 235, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.90", "min_intra_species_ani": "96.75", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000385175.1", "gtdb_species": "s__Salinicoccus albus", "ani": 78.4769, "matched_fragments": 248, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "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": 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qingdaonensis", "ani": 77.5362, "matched_fragments": 127, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "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_900142805.1", "gtdb_species": "s__Salinicoccus alkaliphilus", "ani": 77.0323, "matched_fragments": 117, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus", "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": -0.114, "cell_length": -0.114, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.0, "optimum_ph": 7.5, "genome_size": 2769784.6, "gc_content": 44.5, "coding_genes": 2683.333, "rRNA16S_genes": 4.0, "tRNA_genes": 61.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Salinicoccus", "halodurans" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }