{ "type": "genome", "identifier": "GCF_027706745.1", "organism": "Nocardiopsis suaedae", "title": "Nocardiopsis suaedae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kasetsart University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_027706745.1", "bioproject": "PRJNA224116", "biosample": "SAMN32289976", "wgs_master": "JAQFWP000000000.1", "refseq_category": "reference genome", "taxid": "3018444", "species_taxid": "3018444", "organism_name": "Nocardiopsis suaedae", "infraspecific_name": "strain=LSu2-4", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/01/10", "asm_name": "ASM2770674v1", "asm_submitter": "Kasetsart University", "gbrs_paired_asm": "GCA_027706745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/027/706/745/GCF_027706745.1_ASM2770674v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6970021", "genome_size_ungapped": "6970021", "gc_percent": "73.500000", "replicon_count": "0", "scaffold_count": "140", "contig_count": "140", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_027706745.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "6247", "protein_coding_gene_count": "6124", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-01-10", "dateModified": "2023-01-10", "datePublished": "2023-01-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Nocardiopsis suaedae" ], "sample_taxid": [ "3018444" ], "sample_host_organism": [ "Suaeda maritima" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "1.863 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)": "6970021", "Number of Sequences": "140", "Longest Sequences (bp)": "300741", "N50 (bp)": "80993", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.6", "Number of CDSs": "6328", "Average Protein Length": "316.1", "Coding Ratio (%)": "86.1", "Number of rRNAs": "3", "Number of tRNAs": "63", "Number of CRISPRs": "12" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nocardiopsis chromatogenes", "strain": "strain=YIM 90109", "accession": "GCA_000341185.1", "taxid": 280239, "species_taxid": 280239, "relation_to_type": "type", "validated": true, "ani": 93.1725, "matched_fragments": 1782, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis potens", "strain": "strain=DSM 45234", "accession": "GCA_000341105.1", "taxid": 1246458, "species_taxid": 1246458, "relation_to_type": "type", "validated": true, "ani": 82.8349, "matched_fragments": 1369, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis composta", "strain": "strain=DSM 44551", "accession": "GCA_014200805.1", "taxid": 157465, "species_taxid": 157465, "relation_to_type": "type", "validated": true, "ani": 82.7186, "matched_fragments": 1397, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis mwathae", "strain": "strain=DSM 46659", "accession": "GCA_014201195.1", "taxid": 1472723, "species_taxid": 1472723, "relation_to_type": "type", "validated": true, "ani": 81.039, "matched_fragments": 1029, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis gilva", "strain": "strain=YIM 90087", "accession": "GCA_000341165.1", "taxid": 280236, "species_taxid": 280236, "relation_to_type": "type", "validated": true, "ani": 80.8678, "matched_fragments": 907, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomonospora alba", "strain": "strain=YIM 90003", "accession": "GCA_000826685.1", "taxid": 183763, "species_taxid": 183763, "relation_to_type": "type", "validated": true, "ani": 80.4706, "matched_fragments": 973, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomonospora litoralis", "strain": "strain=M2", "accession": "GCA_004323735.1", "taxid": 2498135, "species_taxid": 2498135, "relation_to_type": "type", "validated": true, "ani": 80.3397, "matched_fragments": 1003, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis sinuspersici", "strain": "strain=UTMC 00102", "accession": "GCA_001998325.1", "taxid": 501010, "species_taxid": 501010, "relation_to_type": "type", "validated": true, "ani": 79.9898, "matched_fragments": 958, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobifida halotolerans", "strain": "strain=DSM 44931", "accession": "GCA_003574835.2", "taxid": 483545, "species_taxid": 483545, "relation_to_type": "type", "validated": true, "ani": 79.835, "matched_fragments": 802, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermobifida alba", "strain": "strain=DSM 43795", "accession": "GCA_023208015.1", "taxid": 53522, "species_taxid": 53522, "relation_to_type": "type", "validated": true, "ani": 79.7844, "matched_fragments": 817, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis flavescens", "strain": "strain=CGMCC 4.5723", "accession": "GCA_900141985.1", "taxid": 758803, "species_taxid": 758803, "relation_to_type": "type", "validated": true, "ani": 79.6724, "matched_fragments": 1065, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis exhalans", "strain": "strain=JCM11759T", "accession": "GCA_024134545.1", "taxid": 163604, "species_taxid": 163604, "relation_to_type": "type", "validated": true, "ani": 79.6022, "matched_fragments": 928, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardiopsis coralli", "strain": "strain=HNM0947", "accession": "GCA_014892575.1", "taxid": 2772213, "species_taxid": 2772213, "relation_to_type": "type", "validated": true, "ani": 79.4678, "matched_fragments": 879, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermomonospora catenispora", "strain": "strain=3-22-3", "accession": "GCA_006363815.1", "taxid": 2493090, "species_taxid": 2493090, "relation_to_type": "type", "validated": true, "ani": 77.7629, "matched_fragments": 684, "total_fragments": 2248, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000341185.1", "gtdb_species": "s__Nocardiopsis_A chromatogenes", "ani": 93.1472, "matched_fragments": 1785, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A", "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_000341245.1", "gtdb_species": "s__Nocardiopsis_A halophila", "ani": 88.642, "matched_fragments": 1614, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000341105.1", "gtdb_species": "s__Nocardiopsis_A potens", "ani": 82.8166, "matched_fragments": 1372, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A", "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_014200805.1", "gtdb_species": "s__Nocardiopsis_A composta", "ani": 82.7783, "matched_fragments": 1386, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A", "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_014201195.1", "gtdb_species": "s__Nocardiopsis_C mwathae", "ani": 81.0584, "matched_fragments": 1026, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C", "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_001552555.1", "gtdb_species": "s__Nocardiopsis_B trehalosi", "ani": 80.8476, "matched_fragments": 1098, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B", "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_013410565.1", "gtdb_species": "s__Streptomonospora nanhaiensis", "ani": 80.8269, "matched_fragments": 1122, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009830945.1", "gtdb_species": "s__Nocardiopsis sp009830945", "ani": 80.0981, "matched_fragments": 978, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.66", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018316655.1", "gtdb_species": "s__Nocardiopsis sp018316655", "ani": 79.7248, "matched_fragments": 1114, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_000515115.1", "gtdb_species": "s__Nocardiopsis sp000515115", "ani": 79.3762, "matched_fragments": 769, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis", "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_014203805.1", "gtdb_species": "s__Lipingzhangella halophila", "ani": 79.1443, "matched_fragments": 864, "total_fragments": 2248, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Lipingzhangella", "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": -0.359, "cell_length": 0.06, "doubling_h": null, "growth_tmp": 28.671, "optimum_tmp": 30.718, "optimum_ph": 8.126, "genome_size": 6294183.832, "gc_content": 71.028, "coding_genes": 5184.289, "rRNA16S_genes": 5.333, "tRNA_genes": 55.833, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": 0.75, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.937, "thermophilic_range_tmp": 0.062, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.352, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.647, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nocardiopsis", "suaedae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }