{ "type": "genome", "identifier": "GCF_024494655.1", "organism": "Halorubrum laminariae", "title": "Halorubrum laminariae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Jiangsu University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_024494655.1", "bioproject": "PRJNA224116", "biosample": "SAMN29911662", "wgs_master": "JANHDL000000000.1", "refseq_category": "reference genome", "taxid": "1433523", "species_taxid": "1433523", "organism_name": "Halorubrum laminariae", "infraspecific_name": "strain=R60", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/30", "asm_name": "ASM2449465v1", "asm_submitter": "Jiangsu University", "gbrs_paired_asm": "GCA_024494655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/494/655/GCF_024494655.1_ASM2449465v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "archaea", "genome_size": "3621885", "genome_size_ungapped": "3621885", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "42", "contig_count": "42", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024494655.1-RS_2024_05_12", "annotation_date": "2024-05-12", "total_gene_count": "3693", "protein_coding_gene_count": "3523", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-07-30", "dateModified": "2022-07-30", "datePublished": "2022-07-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Halorubrum laminariae" ], "sample_taxid": [ "1433523" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Dalian, Liaoning" ], "sample_host_location_id": [], "data_size": "1.004 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)": "3621885", "Number of Sequences": "42", "Longest Sequences (bp)": "609746", "N50 (bp)": "302165", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.9", "Number of CDSs": "3593", "Average Protein Length": "285.9", "Coding Ratio (%)": "85.1", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halorubrum salinum", "strain": "strain=GX71", "accession": "GCA_024494575.1", "taxid": 767517, "species_taxid": 767517, "relation_to_type": "type", "validated": true, "ani": 88.2253, "matched_fragments": 707, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum salipaludis", "strain": "strain=WN019", "accession": "GCA_002286985.1", "taxid": 2032630, "species_taxid": 2032630, "relation_to_type": "type", "validated": true, "ani": 84.0521, "matched_fragments": 675, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum saccharovorum", "strain": "strain=DSM 1137", "accession": "GCA_000337915.1", "taxid": 2248, "species_taxid": 2248, "relation_to_type": "type", "validated": true, "ani": 84.0081, "matched_fragments": 641, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum salsamenti", "strain": "strain=Y69", "accession": "GCA_007671685.1", "taxid": 2583990, "species_taxid": 2583990, "relation_to_type": "type", "validated": true, "ani": 83.9939, "matched_fragments": 659, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum depositum", "strain": "strain=Y78", "accession": "GCA_007671725.1", "taxid": 2583992, "species_taxid": 2583992, "relation_to_type": "type", "validated": true, "ani": 83.9745, "matched_fragments": 646, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum lipolyticum", "strain": "strain=DSM 21995", "accession": "GCA_000337375.1", "taxid": 368624, "species_taxid": 368624, "relation_to_type": "type", "validated": true, "ani": 83.8286, "matched_fragments": 614, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum rutilum", "strain": "strain=YJ-18-S1", "accession": "GCA_024494565.1", "taxid": 1364933, "species_taxid": 1364933, "relation_to_type": "type", "validated": true, "ani": 83.6022, "matched_fragments": 624, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum persicum", "strain": "strain=C49", "accession": "GCA_002727125.1", "taxid": 1383844, "species_taxid": 1383844, "relation_to_type": "type", "validated": true, "ani": 83.5835, "matched_fragments": 662, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum coriense", "strain": "strain=DSM 10284", "accession": "GCA_000337035.1", "taxid": 64713, "species_taxid": 64713, "relation_to_type": "type", "validated": true, "ani": 82.6454, "matched_fragments": 601, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum ezzemoulense", "strain": "strain=DSM 17463", "accession": "GCA_002114285.1", "taxid": 337243, "species_taxid": 337243, "relation_to_type": "type", "validated": true, "ani": 82.5283, "matched_fragments": 614, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halorubrum ezzemoulense", "strain": "strain=DSM 17463", "accession": "GCA_000421805.1", "taxid": 337243, "species_taxid": 337243, "relation_to_type": "type", "validated": true, "ani": 82.4846, "matched_fragments": 626, "total_fragments": 1186, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000746205.1", "gtdb_species": "s__Halorubrum sp000746205", "ani": 87.6948, "matched_fragments": 679, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_003781945.1", "gtdb_species": "s__Halorubrum sp003781945", "ani": 84.1478, "matched_fragments": 654, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_002286985.1", "gtdb_species": "s__Halorubrum sp002286985", "ani": 84.0322, "matched_fragments": 677, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000337915.1", "gtdb_species": "s__Halorubrum saccharovorum", "ani": 84.0114, "matched_fragments": 640, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_007671725.1", "gtdb_species": "s__Halorubrum depositum", "ani": 83.9891, "matched_fragments": 644, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_000337375.1", "gtdb_species": "s__Halorubrum lipolyticum", "ani": 83.805, "matched_fragments": 615, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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": "GCF_002727125.1", "gtdb_species": "s__Halorubrum persicum", "ani": 83.6116, "matched_fragments": 661, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_002252755.1", "gtdb_species": "s__Halorubrum sp002252755", "ani": 83.4998, "matched_fragments": 620, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001261915.1", "gtdb_species": "s__Halorubrum sp001261915", "ani": 83.2174, "matched_fragments": 578, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_900102375.1", "gtdb_species": "s__Halorubrum xinjiangense", "ani": 82.8015, "matched_fragments": 597, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_000337035.1", "gtdb_species": "s__Halorubrum coriense", "ani": 82.6082, "matched_fragments": 605, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "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_002114285.1", "gtdb_species": "s__Halorubrum ezzemoulense", "ani": 82.5966, "matched_fragments": 610, "total_fragments": 1186, "gtdb_taxonomy": "d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "98.29", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.81", "num_clustered_genomes": 17, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.207, "cell_length": 0.287, "doubling_h": 0.945, "growth_tmp": 36.973, "optimum_tmp": 38.687, "optimum_ph": 7.755, "genome_size": 3372661.985, "gc_content": 66.134, "coding_genes": 3172.833, "rRNA16S_genes": 2.5, "tRNA_genes": 49.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.857, "range_salinity": 1.0, "facultative_respiration": 0.13, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.869, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Halorubrum", "laminariae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }