{ "type": "genome", "identifier": "GCF_009901565.1", "organism": "Herbidospora solisilvae", "title": "Herbidospora solisilvae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "School of life science", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009901565.1", "bioproject": "PRJNA224116", "biosample": "SAMN13702288", "wgs_master": "WXEW00000000.1", "refseq_category": "reference genome", "taxid": "2696284", "species_taxid": "2696284", "organism_name": "Herbidospora solisilvae", "infraspecific_name": "strain=NEAU-GS84", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/17", "asm_name": "ASM990156v1", "asm_submitter": "School of life science", "gbrs_paired_asm": "GCA_009901565.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/901/565/GCF_009901565.1_ASM990156v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8374830", "genome_size_ungapped": "8374800", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "27", "contig_count": "27", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009901565.1-RS_2024_12_16", "annotation_date": "2024-12-16", "total_gene_count": "7749", "protein_coding_gene_count": "7597", "non_coding_gene_count": "81", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-01-17", "dateModified": "2020-01-17", "datePublished": "2020-01-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Herbidospora solisilvae" ], "sample_taxid": [ "2696284" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Sanya" ], "sample_host_location_id": [], "data_size": "2.244 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)": "8374830", "Number of Sequences": "27", "Longest Sequences (bp)": "1348287", "N50 (bp)": "685112", "Gap Ratio (%)": "0.000358", "GCcontent (%)": "70.7", "Number of CDSs": "7748", "Average Protein Length": "330.2", "Coding Ratio (%)": "91.7", "Number of rRNAs": "4", "Number of tRNAs": "78", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Herbidospora solisilvae", "strain": "strain=NEAU-GS84", "accession": "GCA_009901565.1", "taxid": 2696284, "species_taxid": 2696284, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2780, "total_fragments": 2781, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Herbidospora galbida", "strain": "strain=NEAU-GS14", "accession": "GCA_005233835.1", "taxid": 2575442, "species_taxid": 2575442, "relation_to_type": "type", "validated": true, "ani": 93.7144, "matched_fragments": 2296, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbidospora sakaeratensis", "strain": "strain=NBRC 102641", "accession": "GCA_001570525.1", "taxid": 564415, "species_taxid": 564415, "relation_to_type": "type", "validated": true, "ani": 93.3717, "matched_fragments": 2349, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbidospora cretacea", "strain": "strain=NBRC 15474", "accession": "GCA_001570605.1", "taxid": 28444, "species_taxid": 28444, "relation_to_type": "type", "validated": true, "ani": 90.4635, "matched_fragments": 2211, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbidospora mongoliensis", "strain": "strain=NBRC 105882", "accession": "GCA_001570545.1", "taxid": 688067, "species_taxid": 688067, "relation_to_type": "type", "validated": true, "ani": 89.5817, "matched_fragments": 2216, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acrocarpospora catenulata", "strain": "strain=H8750", "accession": "GCA_018476525.1", "taxid": 2836182, "species_taxid": 2836182, "relation_to_type": "type", "validated": true, "ani": 81.0387, "matched_fragments": 1490, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea roseoviolacea subsp. carminata", "strain": "strain=DSM 44170", "accession": "GCA_024172185.1", "taxid": 160689, "species_taxid": 103837, "relation_to_type": "type", "validated": true, "ani": 79.5883, "matched_fragments": 1267, "total_fragments": 2781, "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": 79.512, "matched_fragments": 871, "total_fragments": 2781, "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": 79.3273, "matched_fragments": 1278, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptosporangium violaceochromogenes", "strain": "strain=JCM 3281", "accession": "GCA_014654615.1", "taxid": 46188, "species_taxid": 46188, "relation_to_type": "type", "validated": true, "ani": 79.2559, "matched_fragments": 917, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nonomuraea typhae", "strain": "strain=p1410", "accession": "GCA_009760925.1", "taxid": 2603600, "species_taxid": 2603600, "relation_to_type": "type", "validated": true, "ani": 78.8703, "matched_fragments": 1284, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bowdeniella nasicola", "strain": "strain=DSM 19116", "accession": "GCA_001907295.1", "taxid": 208480, "species_taxid": 208480, "relation_to_type": "type", "validated": true, "ani": 76.2005, "matched_fragments": 127, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Isoptericola chiayiensis", "strain": "strain=KCTC 19740", "accession": "GCA_013149805.1", "taxid": 579446, "species_taxid": 579446, "relation_to_type": "type", "validated": true, "ani": 75.9581, "matched_fragments": 412, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cryobacterium soli", "strain": "strain=GCJ02", "accession": "GCA_003611035.1", "taxid": 2220095, "species_taxid": 2220095, "relation_to_type": "type", "validated": true, "ani": 75.7865, "matched_fragments": 308, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus jenensis", "strain": "strain=DSM 9580", "accession": "GCA_003752465.1", "taxid": 46353, "species_taxid": 46353, "relation_to_type": "type", "validated": true, "ani": 75.7826, "matched_fragments": 321, "total_fragments": 2781, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009901565.1", "gtdb_species": "s__Herbidospora solisilvae", "ani": 100.0, "matched_fragments": 2780, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.93", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001570565.1", "gtdb_species": "s__Herbidospora yilanensis", "ani": 94.5861, "matched_fragments": 2229, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora", "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_005233835.1", "gtdb_species": "s__Herbidospora galbida", "ani": 93.7235, "matched_fragments": 2295, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora", "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_001570525.1", "gtdb_species": "s__Herbidospora sakaeratensis", "ani": 93.3687, "matched_fragments": 2350, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora", "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_001570585.1", "gtdb_species": "s__Herbidospora daliensis", "ani": 92.9885, "matched_fragments": 2368, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora", "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_001570605.1", "gtdb_species": "s__Herbidospora cretacea", "ani": 90.4467, "matched_fragments": 2214, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora", "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_002262875.1", "gtdb_species": "s__Amycolatopsis antarctica", "ani": 75.8683, "matched_fragments": 465, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis", "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": "GCA_017302295.1", "gtdb_species": "s__Thauera sp017302295", "ani": 74.9604, "matched_fragments": 147, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera", "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": "GCA_017853245.1", "gtdb_species": "s__FEB-7 sp017853245", "ani": 74.9527, "matched_fragments": 54, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7", "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": "GCA_016861105.1", "gtdb_species": "s__VBCG01 sp016861105", "ani": 74.8517, "matched_fragments": 307, "total_fragments": 2781, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.35, "optimum_ph": null, "genome_size": 8458323.033, "gc_content": 70.498, "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": 1.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Herbidospora", "solisilvae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }