{ "type": "genome", "identifier": "GCF_003001935.1", "organism": "Nonomuraea fuscirosea", "title": "Nonomuraea fuscirosea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003001935.1", "bioproject": "PRJNA224116", "biosample": "SAMN06297061", "wgs_master": "PVNG00000000.1", "refseq_category": "na", "taxid": "1291556", "species_taxid": "1291556", "organism_name": "Nonomuraea fuscirosea", "infraspecific_name": "strain=CGMCC 4.7104", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/15", "asm_name": "ASM300193v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003001935.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/001/935/GCF_003001935.1_ASM300193v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "12180574", "genome_size_ungapped": "12180574", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "93", "contig_count": "93", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003001935.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "11302", "protein_coding_gene_count": "11089", "non_coding_gene_count": "79", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-15", "dateModified": "2018-03-15", "datePublished": "2018-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Nonomuraea fuscirosea" ], "sample_taxid": [ "1291556" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "3.273 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 99.07, "contamination": 6.6, "strain_heterogeneity": 40.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "12180574", "Number of Sequences": "93", "Longest Sequences (bp)": "809247", "N50 (bp)": "363978", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.0", "Number of CDSs": "11523", "Average Protein Length": "313.6", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "85", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nonomuraea fuscirosea", "strain": "strain=CGMCC 4.7104", "accession": "GCA_003001935.1", "taxid": 1291556, "species_taxid": 1291556, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 4005, "total_fragments": 4012, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nonomuraea rubra", "strain": "strain=DSM 43768", "accession": "GCA_014207985.1", "taxid": 46180, "species_taxid": 46180, "relation_to_type": "type", "validated": true, "ani": 87.0507, "matched_fragments": 2742, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea candida", "strain": "strain=NRRL B-24552", "accession": "GCA_000725485.1", "taxid": 359159, "species_taxid": 359159, "relation_to_type": "type", "validated": true, "ani": 86.8543, "matched_fragments": 2429, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea solani", "strain": "strain=CGMCC 4.7037", "accession": "GCA_900108335.1", "taxid": 1144553, "species_taxid": 1144553, "relation_to_type": "type", "validated": true, "ani": 86.3443, "matched_fragments": 2617, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea zeae", "strain": "strain=DSM 100528", "accession": "GCA_005889725.1", "taxid": 1642303, "species_taxid": 1642303, "relation_to_type": "type", "validated": true, "ani": 85.8028, "matched_fragments": 2472, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea aridisoli", "strain": "strain=KC333", "accession": "GCA_003236395.1", "taxid": 2070368, "species_taxid": 2070368, "relation_to_type": "type", "validated": true, "ani": 85.6698, "matched_fragments": 2029, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea jabiensis", "strain": "strain=DSM 45507", "accession": "GCA_014204795.1", "taxid": 882448, "species_taxid": 882448, "relation_to_type": "type", "validated": true, "ani": 85.4392, "matched_fragments": 2554, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea angiospora", "strain": "strain=DSM 43173", "accession": "GCA_014873145.1", "taxid": 46172, "species_taxid": 46172, "relation_to_type": "type", "validated": true, "ani": 85.3998, "matched_fragments": 2578, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea phyllanthi", "strain": "strain=WYY166", "accession": "GCA_009497075.1", "taxid": 2219224, "species_taxid": 2219224, "relation_to_type": "type", "validated": true, "ani": 85.2529, "matched_fragments": 2412, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea phyllanthi", "strain": "strain=PA1-10", "accession": "GCA_006334985.2", "taxid": 2219224, "species_taxid": 2219224, "relation_to_type": "type", "validated": true, "ani": 85.2249, "matched_fragments": 2386, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea basaltis", "strain": "strain=160415", "accession": "GCA_005893125.1", "taxid": 2495887, "species_taxid": 2495887, "relation_to_type": "type", "validated": true, "ani": 85.0391, "matched_fragments": 2334, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea coxensis", "strain": "strain=DSM 45129", "accession": "GCA_000379885.1", "taxid": 404386, "species_taxid": 404386, "relation_to_type": "type", "validated": true, "ani": 84.8752, "matched_fragments": 2115, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea coxensis", "strain": "strain=DSM 45129", "accession": "GCA_019397265.1", "taxid": 404386, "species_taxid": 404386, "relation_to_type": "type", "validated": true, "ani": 84.7708, "matched_fragments": 2159, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea spiralis", "strain": "strain=JCM 3286", "accession": "GCA_014648435.1", "taxid": 46182, "species_taxid": 46182, "relation_to_type": "type", "validated": true, "ani": 84.2886, "matched_fragments": 2201, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea rhizosphaerae", "strain": "strain=CGMCC 4.7431", "accession": "GCA_019396405.1", "taxid": 2665663, "species_taxid": 2665663, "relation_to_type": "type", "validated": true, "ani": 84.0367, "matched_fragments": 1296, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea aurantiaca", "strain": "strain=NEAU-L178", "accession": "GCA_020215705.1", "taxid": 2878562, "species_taxid": 2878562, "relation_to_type": "type", "validated": true, "ani": 82.9809, "matched_fragments": 2169, "total_fragments": 4012, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 99.07, "contamination": 6.6, "strain_heterogeneity": 40.0 }, "gtdb_result": [ { "accession": "GCF_003001935.1", "gtdb_species": "s__Nonomuraea fuscirosea", "ani": 100.0, "matched_fragments": 4005, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_014207985.1", "gtdb_species": "s__Nonomuraea rubra", "ani": 87.0371, "matched_fragments": 2746, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_000725485.1", "gtdb_species": "s__Nonomuraea candida", "ani": 86.8123, "matched_fragments": 2437, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_008086045.1", "gtdb_species": "s__Nonomuraea sp008086045", "ani": 86.5673, "matched_fragments": 2629, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_900323885.1", "gtdb_species": "s__Nonomuraea parvosata", "ani": 86.4776, "matched_fragments": 2677, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.29", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900108335.1", "gtdb_species": "s__Nonomuraea solani", "ani": 86.3267, "matched_fragments": 2620, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_005889725.1", "gtdb_species": "s__Nonomuraea zeae", "ani": 85.8048, "matched_fragments": 2472, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_014204795.1", "gtdb_species": "s__Nonomuraea jabiensis", "ani": 85.4755, "matched_fragments": 2543, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_014873145.1", "gtdb_species": "s__Nonomuraea angiospora", "ani": 85.4288, "matched_fragments": 2572, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_005893125.1", "gtdb_species": "s__Nonomuraea sp005893125", "ani": 85.0278, "matched_fragments": 2335, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_000379885.1", "gtdb_species": "s__Nonomuraea coxensis", "ani": 84.8507, "matched_fragments": 2123, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "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_014648435.1", "gtdb_species": "s__Nonomuraea spiralis", "ani": 84.2685, "matched_fragments": 2205, "total_fragments": 4012, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.03", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.092, "cell_length": 0.155, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.687, "optimum_ph": 6.857, "genome_size": 12180574.0, "gc_content": 72.2, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": null, "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": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Nonomuraea", "fuscirosea" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }