{ "type": "genome", "identifier": "GCF_009900715.1", "organism": "Halococcus salsus", "title": "Halococcus salsus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Anhui Normal University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009900715.1", "bioproject": "PRJNA224116", "biosample": "SAMN13783723", "wgs_master": "JAAAJC000000000.1", "refseq_category": "reference genome", "taxid": "2162894", "species_taxid": "2162894", "organism_name": "Halococcus salsus", "infraspecific_name": "strain=ZJ1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/17", "asm_name": "ASM990071v1", "asm_submitter": "Anhui Normal University", "gbrs_paired_asm": "GCA_009900715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/900/715/GCF_009900715.1_ASM990071v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3521978", "genome_size_ungapped": "3521843", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "30", "contig_count": "30", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009900715.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3622", "protein_coding_gene_count": "3511", "non_coding_gene_count": "54", "pubmed_id": "30311879" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-01-17", "dateModified": "2020-01-17", "datePublished": "2020-01-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Halococcus salsus" ], "sample_taxid": [ "2162894" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Yunnan" ], "sample_host_location_id": [], "data_size": "0.964 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3521978", "Number of Sequences": "30", "Longest Sequences (bp)": "1384276", "N50 (bp)": "472564", "Gap Ratio (%)": "0.004259", "GCcontent (%)": "64.7", "Number of CDSs": "3546", "Average Protein Length": "280.3", "Coding Ratio (%)": "84.7", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halococcus salsus", "strain": "strain=ZJ1", "accession": "GCA_009900715.1", "taxid": 2162894, "species_taxid": 2162894, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1161, "total_fragments": 1161, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halococcus hamelinensis", "strain": "strain=100A6", "accession": "GCA_000336675.1", "taxid": 332168, "species_taxid": 332168, "relation_to_type": "type", "validated": true, "ani": 92.4346, "matched_fragments": 864, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus hamelinensis", "strain": "strain=100A6", "accession": "GCA_000259215.1", "taxid": 332168, "species_taxid": 332168, "relation_to_type": "type", "validated": true, "ani": 92.2639, "matched_fragments": 763, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus morrhuae", "strain": "strain=DSM 1307", "accession": "GCA_000336695.1", "taxid": 2250, "species_taxid": 2250, "relation_to_type": "type", "validated": true, "ani": 80.3275, "matched_fragments": 520, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus qingdaonensis", "strain": "strain=CGMCC 1.4243", "accession": "GCA_024508235.1", "taxid": 224402, "species_taxid": 224402, "relation_to_type": "type", "validated": true, "ani": 80.1375, "matched_fragments": 536, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus saccharolyticus", "strain": "strain=DSM 5350", "accession": "GCA_000336915.1", "taxid": 62319, "species_taxid": 62319, "relation_to_type": "type", "validated": true, "ani": 79.9378, "matched_fragments": 532, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halosimplex halophilum", "strain": "strain=TH32", "accession": "GCA_004698125.1", "taxid": 2559572, "species_taxid": 2559572, "relation_to_type": "type", "validated": true, "ani": 77.183, "matched_fragments": 382, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorientalis litorea", "strain": "strain=ZY14", "accession": "GCA_023028225.1", "taxid": 2931977, "species_taxid": 2931977, "relation_to_type": "type", "validated": true, "ani": 76.9633, "matched_fragments": 243, "total_fragments": 1161, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009900715.1", "gtdb_species": "s__Halococcus salsus", "ani": 100.0, "matched_fragments": 1161, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.85", "min_intra_species_ani": "95.85", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000336675.1", "gtdb_species": "s__Halococcus hamelinensis", "ani": 92.455, "matched_fragments": 863, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000336695.1", "gtdb_species": "s__Halococcus morrhuae", "ani": 80.3175, "matched_fragments": 521, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "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_000334895.1", "gtdb_species": "s__Halococcus agarilyticus", "ani": 80.1386, "matched_fragments": 586, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "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_000755245.1", "gtdb_species": "s__Halococcus sediminicola", "ani": 80.069, "matched_fragments": 584, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "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_000336915.1", "gtdb_species": "s__Halococcus saccharolyticus", "ani": 79.9005, "matched_fragments": 535, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "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_004698125.1", "gtdb_species": "s__Halosimplex halophilum", "ani": 77.1899, "matched_fragments": 382, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex", "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_017094525.1", "gtdb_species": "s__Halapricum sp017094525", "ani": 76.9695, "matched_fragments": 209, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "98.12", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003021235.1", "gtdb_species": "s__Halococcus sp003021235", "ani": 76.9583, "matched_fragments": 277, "total_fragments": 1161, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "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": -0.097, "cell_length": -0.097, "doubling_h": 1.041, "growth_tmp": 38.4, "optimum_tmp": 36.416, "optimum_ph": 7.075, "genome_size": 3621932.0, "gc_content": 62.3, "coding_genes": null, "rRNA16S_genes": 2.0, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Halococcus", "salsus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }