{ "type": "genome", "identifier": "GCF_000259215.1", "organism": "Halococcus hamelinensis 100A6", "title": "Halococcus hamelinensis 100A6", "description": "na", "data type": "Genome sequencing and assembly", "organization": "School of Biotechnology and Biomolecular Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000259215.1", "bioproject": "PRJNA224116", "biosample": "SAMN02470884", "wgs_master": "AJRK00000000.1", "refseq_category": "na", "taxid": "1132509", "species_taxid": "332168", "organism_name": "Halococcus hamelinensis 100A6", "infraspecific_name": "strain=100A6", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/04/18", "asm_name": "ASM25921v1", "asm_submitter": "School of Biotechnology and Biomolecular Sciences", "gbrs_paired_asm": "GCA_000259215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/259/215/GCF_000259215.1_ASM25921v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3383679", "genome_size_ungapped": "3383679", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "453", "contig_count": "453", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000259215.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "3651", "protein_coding_gene_count": "3442", "non_coding_gene_count": "51", "pubmed_id": "22461544" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-04-18", "dateModified": "2012-04-18", "datePublished": "2012-04-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Halococcus hamelinensis 100A6" ], "sample_taxid": [ "1132509" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Australia: Shark Bay, Hamelin Pool" ], "sample_host_location_id": [], "data_size": "0.933 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 8.33, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3383679", "Number of Sequences": "453", "Longest Sequences (bp)": "105929", "N50 (bp)": "18000", "Gap Ratio (%)": "0.000059", "GCcontent (%)": "65.5", "Number of CDSs": "3165", "Average Protein Length": "273.0", "Coding Ratio (%)": "76.6", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halococcus hamelinensis", "strain": "strain=100A6", "accession": "GCA_000259215.1", "taxid": 332168, "species_taxid": 332168, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 942, "total_fragments": 952, "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": 99.9566, "matched_fragments": 933, "total_fragments": 952, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halococcus salsus", "strain": "strain=ZJ1", "accession": "GCA_009900715.1", "taxid": 2162894, "species_taxid": 2162894, "relation_to_type": "type", "validated": true, "ani": 92.3874, "matched_fragments": 777, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus thailandensis", "strain": "strain=JCM 13552", "accession": "GCA_000336715.1", "taxid": 335952, "species_taxid": 335952, "relation_to_type": "type", "validated": true, "ani": 80.3546, "matched_fragments": 483, "total_fragments": 952, "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": 80.3066, "matched_fragments": 464, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus sediminicola", "strain": "strain=CBA1101", "accession": "GCA_000755245.1", "taxid": 1264579, "species_taxid": 1264579, "relation_to_type": "type", "validated": true, "ani": 80.0119, "matched_fragments": 501, "total_fragments": 952, "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": 79.9159, "matched_fragments": 468, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus salifodinae", "strain": "strain=DSM 8989", "accession": "GCA_000336935.1", "taxid": 36738, "species_taxid": 36738, "relation_to_type": "type", "validated": true, "ani": 79.7341, "matched_fragments": 516, "total_fragments": 952, "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": 77.1957, "matched_fragments": 367, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 8.33, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000336675.1", "gtdb_species": "s__Halococcus hamelinensis", "ani": 99.9566, "matched_fragments": 933, "total_fragments": 952, "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": "conclusive" }, { "accession": "GCF_009900715.1", "gtdb_species": "s__Halococcus salsus", "ani": 92.3874, "matched_fragments": 777, "total_fragments": 952, "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": "-" }, { "accession": "GCF_000334895.1", "gtdb_species": "s__Halococcus agarilyticus", "ani": 80.4759, "matched_fragments": 518, "total_fragments": 952, "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_000336715.1", "gtdb_species": "s__Halococcus thailandensis", "ani": 80.3364, "matched_fragments": 485, "total_fragments": 952, "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": 80.055, "matched_fragments": 497, "total_fragments": 952, "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": "GCA_003022685.1", "gtdb_species": "s__Halococcus sp003022685", "ani": 79.9264, "matched_fragments": 373, "total_fragments": 952, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halococcaceae;g__Halococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.70", "min_intra_species_ani": "95.70", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.79", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000336915.1", "gtdb_species": "s__Halococcus saccharolyticus", "ani": 79.9256, "matched_fragments": 468, "total_fragments": 952, "gtdb_taxonomy": 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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", "hamelinensis", "100A6" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }