{ "type": "genome", "identifier": "GCF_900116135.1", "organism": "Saccharopolyspora flava", "title": "Saccharopolyspora flava", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900116135.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660874", "wgs_master": "FOZX00000000.1", "refseq_category": "reference genome", "taxid": "95161", "species_taxid": "95161", "organism_name": "Saccharopolyspora flava", "infraspecific_name": "strain=DSM 44771", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/05", "asm_name": "IMG-taxon 2599185150 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900116135.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/116/135/GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6291299", "genome_size_ungapped": "6291109", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "22", "contig_count": "22", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900116135.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "5710", "protein_coding_gene_count": "5615", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-05", "dateModified": "2016-11-05", "datePublished": "2016-11-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Saccharopolyspora flava" ], "sample_taxid": [ "95161" ], "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": "1.673 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)": "6291299", "Number of Sequences": "22", "Longest Sequences (bp)": "1461917", "N50 (bp)": "505605", "Gap Ratio (%)": "0.003020", "GCcontent (%)": "70.8", "Number of CDSs": "5709", "Average Protein Length": "327.1", "Coding Ratio (%)": "89.1", "Number of rRNAs": "4", "Number of tRNAs": "65", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Saccharopolyspora flava", "strain": "strain=DSM 44771", "accession": "GCA_900116135.1", "taxid": 95161, "species_taxid": 95161, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2085, "total_fragments": 2085, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Saccharopolyspora endophytica", "strain": "strain=KCTC 19397", "accession": "GCA_018070075.1", "taxid": 543886, "species_taxid": 543886, "relation_to_type": "type", "validated": true, "ani": 89.3964, "matched_fragments": 1682, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora terrae", "strain": "strain=16K309", "accession": "GCA_004348435.1", "taxid": 2530384, "species_taxid": 2530384, "relation_to_type": "type", "validated": true, "ani": 89.351, "matched_fragments": 1609, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora karakumensis", "strain": "strain=5K548", "accession": "GCA_004349225.1", "taxid": 2530386, "species_taxid": 2530386, "relation_to_type": "type", "validated": true, "ani": 89.3462, "matched_fragments": 1573, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora rhizosphaerae", "strain": "strain=H219", "accession": "GCA_003931915.1", "taxid": 2492662, "species_taxid": 2492662, "relation_to_type": "type", "validated": true, "ani": 88.5773, "matched_fragments": 1538, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora aridisoli", "strain": "strain=16K404", "accession": "GCA_004348445.1", "taxid": 2530385, "species_taxid": 2530385, "relation_to_type": "type", "validated": true, "ani": 88.506, "matched_fragments": 1604, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharopolyspora dendranthemae", "strain": "strain=DSM 46699", "accession": "GCA_007829955.1", "taxid": 1181886, "species_taxid": 1181886, "relation_to_type": "type", "validated": true, "ani": 87.9881, "matched_fragments": 1703, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopolyspora algeriensis", "strain": "strain=CECT 8575", "accession": "GCA_003337235.1", "taxid": 1500506, "species_taxid": 1500506, "relation_to_type": "type", "validated": true, "ani": 79.2669, "matched_fragments": 703, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopolyspora algeriensis", "strain": "strain=DSM 46680", "accession": "GCA_006716575.1", "taxid": 1500506, "species_taxid": 1500506, "relation_to_type": "type", "validated": true, "ani": 79.2093, "matched_fragments": 696, "total_fragments": 2085, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900116135.1", "gtdb_species": "s__Saccharopolyspora flava", "ani": 100.0, "matched_fragments": 2085, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora", "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_018070075.1", "gtdb_species": "s__Saccharopolyspora endophytica", "ani": 89.3828, "matched_fragments": 1683, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.33", "min_intra_species_ani": "95.95", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003931915.1", "gtdb_species": "s__Saccharopolyspora rhizosphaerae", "ani": 88.5566, "matched_fragments": 1540, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora", "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_004348445.1", "gtdb_species": "s__Saccharopolyspora sp004348445", "ani": 88.5491, "matched_fragments": 1600, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora", "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_007829955.1", "gtdb_species": "s__Saccharopolyspora dendranthemae", "ani": 87.9813, "matched_fragments": 1704, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora", "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_014137975.1", "gtdb_species": "s__Halosaccharopolyspora lacisalsi", "ani": 79.4889, "matched_fragments": 793, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halosaccharopolyspora", "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_003337235.1", "gtdb_species": "s__Halopolyspora algeriensis", "ani": 79.2599, "matched_fragments": 704, "total_fragments": 2085, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halopolyspora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.318, "cell_length": 0.096, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.0, "optimum_ph": 7.178, "genome_size": 6291299.0, "gc_content": 67.94, "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": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.833, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.166, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Saccharopolyspora", "flava" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }