{ "type": "genome", "identifier": "GCF_000755245.1", "organism": "Halococcus sediminicola", "title": "Halococcus sediminicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea Basic Science Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000755245.1", "bioproject": "PRJNA224116", "biosample": "SAMD00019895", "wgs_master": "BBMP00000000.1", "refseq_category": "reference genome", "taxid": "1264579", "species_taxid": "1264579", "organism_name": "Halococcus sediminicola", "infraspecific_name": "strain=CBA1101", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/09/11", "asm_name": "ASM75524v1", "asm_submitter": "Korea Basic Science Institute", "gbrs_paired_asm": "GCA_000755245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/755/245/GCF_000755245.1_ASM75524v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3764367", "genome_size_ungapped": "3764367", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "27", "contig_count": "27", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000755245.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "3882", "protein_coding_gene_count": "3696", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-09-11", "dateModified": "2014-09-11", "datePublished": "2014-09-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Halococcus sediminicola" ], "sample_taxid": [ "1264579" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: The bay of Gangjin" ], "sample_host_location_id": [], "data_size": "1.045 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)": "3764367", "Number of Sequences": "27", "Longest Sequences (bp)": "974711", "N50 (bp)": "275599", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.3", "Number of CDSs": "3850", "Average Protein Length": "280.2", "Coding Ratio (%)": "86.0", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halococcus sediminicola", "strain": "strain=CBA1101", "accession": "GCA_000755245.1", "taxid": 1264579, "species_taxid": 1264579, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1240, "total_fragments": 1241, "ani_threshold": 95, "status": "conclusive" }, { "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": 86.2176, "matched_fragments": 718, "total_fragments": 1241, "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": 85.8341, "matched_fragments": 696, "total_fragments": 1241, "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": 85.7123, "matched_fragments": 749, "total_fragments": 1241, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halococcus dombrowskii", "strain": "strain=H4", "accession": "GCA_022870485.1", "taxid": 179637, "species_taxid": 179637, "relation_to_type": "type", "validated": true, "ani": 85.5331, "matched_fragments": 798, "total_fragments": 1241, "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": 79.7982, "matched_fragments": 585, "total_fragments": 1241, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000755245.1", "gtdb_species": "s__Halococcus sediminicola", "ani": 100.0, "matched_fragments": 1240, "total_fragments": 1241, "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": "conclusive" }, { "accession": "GCF_000336695.1", "gtdb_species": "s__Halococcus morrhuae", "ani": 85.8453, "matched_fragments": 698, "total_fragments": 1241, "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": 85.7367, "matched_fragments": 747, "total_fragments": 1241, "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_000336935.1", "gtdb_species": "s__Halococcus salifodinae", "ani": 80.4256, "matched_fragments": 629, "total_fragments": 1241, "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": 80.2916, "matched_fragments": 570, "total_fragments": 1241, "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_009900715.1", "gtdb_species": "s__Halococcus salsus", "ani": 80.2552, "matched_fragments": 567, "total_fragments": 1241, "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_000336675.1", "gtdb_species": "s__Halococcus hamelinensis", "ani": 80.1401, "matched_fragments": 553, "total_fragments": 1241, "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_000336915.1", "gtdb_species": "s__Halococcus saccharolyticus", "ani": 79.7769, "matched_fragments": 587, "total_fragments": 1241, "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_004799665.1", "gtdb_species": "s__Halapricum salinum", "ani": 77.0015, "matched_fragments": 221, "total_fragments": 1241, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum", "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": "-" }, { "accession": "GCA_003022085.1", "gtdb_species": "s__Halovenus sp003022085", "ani": 76.0234, "matched_fragments": 91, "total_fragments": 1241, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus", "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": 37.5, "optimum_ph": 7.075, "genome_size": 3764367.0, "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", "sediminicola" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }