{ "type": "genome", "identifier": "GCF_000336695.1", "organism": "Halococcus morrhuae DSM 1307", "title": "Halococcus morrhuae DSM 1307", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of California, Davis", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000336695.1", "bioproject": "PRJNA224116", "biosample": "SAMN02471675", "wgs_master": "AOMC00000000.1", "refseq_category": "reference genome", "taxid": "931277", "species_taxid": "2250", "organism_name": "Halococcus morrhuae DSM 1307", "infraspecific_name": "strain=DSM 1307", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/02/04", "asm_name": "ASM33669v1", "asm_submitter": "University of California, Davis", "gbrs_paired_asm": "GCA_000336695.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/336/695/GCF_000336695.1_ASM33669v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "2991556", "genome_size_ungapped": "2991556", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "167", "contig_count": "167", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000336695.1-RS_2024_10_21", "annotation_date": "2024-10-21", "total_gene_count": "3128", "protein_coding_gene_count": "2936", "non_coding_gene_count": "49", "pubmed_id": "25393412" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-02-04", "dateModified": "2013-02-04", "datePublished": "2013-02-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Halococcus morrhuae DSM 1307" ], "sample_taxid": [ "931277" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.827 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2991556", "Number of Sequences": "167", "Longest Sequences (bp)": "200468", "N50 (bp)": "70502", "Gap Ratio (%)": "0.009259", "GCcontent (%)": "63.8", "Number of CDSs": "2983", "Average Protein Length": "281.3", "Coding Ratio (%)": "84.1", "Number of rRNAs": "3", "Number of tRNAs": "45", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halococcus morrhuae", "strain": "strain=DSM 1307", "accession": "GCA_000336695.1", "taxid": 2250, "species_taxid": 2250, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 917, "total_fragments": 923, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Halococcus dombrowskii", "strain": "strain=H4", "accession": "GCA_022870485.1", "taxid": 179637, "species_taxid": 179637, "relation_to_type": "type", "validated": true, "ani": 96.3448, "matched_fragments": 834, "total_fragments": 923, "ani_threshold": 95, "status": "inconclusive" }, { "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": 93.0378, "matched_fragments": 769, "total_fragments": 923, "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": 92.8345, "matched_fragments": 790, "total_fragments": 923, "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": 85.924, "matched_fragments": 702, "total_fragments": 923, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000336695.1", "gtdb_species": "s__Halococcus morrhuae", "ani": 100.0, "matched_fragments": 917, "total_fragments": 923, "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_000336715.1", "gtdb_species": "s__Halococcus thailandensis", "ani": 92.8271, "matched_fragments": 790, "total_fragments": 923, "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": 85.9404, "matched_fragments": 702, "total_fragments": 923, "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": 80.5509, "matched_fragments": 545, "total_fragments": 923, "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": 80.2495, "matched_fragments": 529, "total_fragments": 923, "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": 80.1831, "matched_fragments": 496, "total_fragments": 923, "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": "GCA_003022685.1", "gtdb_species": "s__Halococcus sp003022685", "ani": 80.1131, "matched_fragments": 386, "total_fragments": 923, "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": 80.0397, "matched_fragments": 530, "total_fragments": 923, "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": 0.164, "growth_tmp": 44.0, "optimum_tmp": 37.0, "optimum_ph": 7.075, "genome_size": 2991556.0, "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", "morrhuae", "DSM", "1307" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }