{ "type": "genome", "identifier": "GCF_002869765.1", "organism": "Deinococcus planocerae", "title": "Deinococcus planocerae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shenzhen University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002869765.1", "bioproject": "PRJNA224116", "biosample": "SAMN04914635", "wgs_master": "PNOR00000000.1", "refseq_category": "reference genome", "taxid": "1737569", "species_taxid": "1737569", "organism_name": "Deinococcus planocerae", "infraspecific_name": "strain=XY-FW106", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/01/09", "asm_name": "ASM286976v1", "asm_submitter": "Shenzhen University", "gbrs_paired_asm": "GCA_002869765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/869/765/GCF_002869765.1_ASM286976v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4314847", "genome_size_ungapped": "4314847", "gc_percent": "70.000000", "replicon_count": "0", "scaffold_count": "96", "contig_count": "96", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002869765.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "4321", "protein_coding_gene_count": "4184", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-01-09", "dateModified": "2018-01-09", "datePublished": "2018-01-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Deinococcus planocerae" ], "sample_taxid": [ "1737569" ], "sample_host_organism": [ "Planocera reticulata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Hong Kong: Sai Kung" ], "sample_host_location_id": [], "data_size": "1.177 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4314847", "Number of Sequences": "96", "Longest Sequences (bp)": "224504", "N50 (bp)": "108247", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.2", "Number of CDSs": "4238", "Average Protein Length": "295.7", "Coding Ratio (%)": "87.1", "Number of rRNAs": "0", "Number of tRNAs": "59", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Deinococcus planocerae", "strain": "strain=XY-FW106", "accession": "GCA_002869765.1", "taxid": 1737569, "species_taxid": 1737569, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1387, "total_fragments": 1392, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Deinococcus aerius", "strain": "strain=TR0125", "accession": "GCA_002897375.1", "taxid": 200253, "species_taxid": 200253, "relation_to_type": "type", "validated": true, "ani": 84.7167, "matched_fragments": 949, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus metallilatus", "strain": "strain=MA1002", "accession": "GCA_004115945.1", "taxid": 1211322, "species_taxid": 1211322, "relation_to_type": "type", "validated": true, "ani": 83.3069, "matched_fragments": 823, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus metallilatus", "strain": "strain=MA1002", "accession": "GCA_004758605.1", "taxid": 1211322, "species_taxid": 1211322, "relation_to_type": "type", "validated": true, "ani": 83.2238, "matched_fragments": 847, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus metallilatus", "strain": "strain=DSM 105434", "accession": "GCA_014202095.1", "taxid": 1211322, "species_taxid": 1211322, "relation_to_type": "type", "validated": true, "ani": 83.1187, "matched_fragments": 845, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus apachensis", "strain": "strain=DSM 19763", "accession": "GCA_000381345.1", "taxid": 309886, "species_taxid": 309886, "relation_to_type": "type", "validated": true, "ani": 82.8511, "matched_fragments": 827, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus budaensis", "strain": "strain=DSM 101791", "accession": "GCA_014201885.1", "taxid": 1665626, "species_taxid": 1665626, "relation_to_type": "type", "validated": true, "ani": 82.3233, "matched_fragments": 796, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus terrestris", "strain": "strain=SDU3-2", "accession": "GCA_009377345.1", "taxid": 2651870, "species_taxid": 2651870, "relation_to_type": "type", "validated": true, "ani": 81.6808, "matched_fragments": 703, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus phoenicis", "strain": "strain=1P10ME", "accession": "GCA_000599865.1", "taxid": 1476583, "species_taxid": 1476583, "relation_to_type": "type", "validated": true, "ani": 81.6807, "matched_fragments": 748, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus actinosclerus", "strain": "strain=BM2", "accession": "GCA_001507665.1", "taxid": 1768108, "species_taxid": 1768108, "relation_to_type": "type", "validated": true, "ani": 79.0941, "matched_fragments": 567, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deinococcus kurensis", "strain": "strain=KR-1", "accession": "GCA_009687825.1", "taxid": 2662757, "species_taxid": 2662757, "relation_to_type": "type", "validated": true, "ani": 78.9569, "matched_fragments": 644, "total_fragments": 1392, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002869765.1", "gtdb_species": "s__Deinococcus planocerae", "ani": 100.0, "matched_fragments": 1387, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_018863415.1", "gtdb_species": "s__Deinococcus sp018863415", "ani": 90.8011, "matched_fragments": 1093, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_002897375.1", "gtdb_species": "s__Deinococcus aerius", "ani": 84.7487, "matched_fragments": 946, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_004758605.1", "gtdb_species": "s__Deinococcus metallilatus", "ani": 83.1842, "matched_fragments": 852, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000381345.1", "gtdb_species": "s__Deinococcus apachensis", "ani": 82.8605, "matched_fragments": 826, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_014201885.1", "gtdb_species": "s__Deinococcus budaensis", "ani": 82.3476, "matched_fragments": 794, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_002953415.1", "gtdb_species": "s__Deinococcus sp002953415", "ani": 81.8453, "matched_fragments": 724, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_000599865.1", "gtdb_species": "s__Deinococcus phoenicis", "ani": 81.7002, "matched_fragments": 746, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_002901445.1", "gtdb_species": "s__Deinococcus koreensis", "ani": 79.5085, "matched_fragments": 642, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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_001507665.1", "gtdb_species": "s__Deinococcus actinosclerus", "ani": 79.1191, "matched_fragments": 564, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.26", "min_intra_species_ani": "96.21", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001949125.1", "gtdb_species": "s__Deinococcus marmoris_A", "ani": 78.1023, "matched_fragments": 509, "total_fragments": 1392, "gtdb_taxonomy": "d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus", "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": 0.051, "cell_length": 0.196, "doubling_h": 0.111, "growth_tmp": 28.619, "optimum_tmp": 29.066, "optimum_ph": 7.156, "genome_size": 4107692.879, "gc_content": 65.729, "coding_genes": 3268.576, "rRNA16S_genes": 3.545, "tRNA_genes": 48.236, "gram_stain": 0.977, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.028, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.971, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.3, "coccus_cell_shape": 0.7, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Deinococcus", "planocerae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }