{ "type": "genome", "identifier": "GCF_004349235.1", "organism": "Actinomadura darangshiensis", "title": "Actinomadura darangshiensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ondokuz Mayis University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004349235.1", "bioproject": "PRJNA224116", "biosample": "SAMN11032560", "wgs_master": "SMKY00000000.1", "refseq_category": "reference genome", "taxid": "705336", "species_taxid": "705336", "organism_name": "Actinomadura darangshiensis", "infraspecific_name": "strain=DSM 45941", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/13", "asm_name": "ASM434923v1", "asm_submitter": "Ondokuz Mayis University", "gbrs_paired_asm": "GCA_004349235.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/349/235/GCF_004349235.1_ASM434923v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "9886063", "genome_size_ungapped": "9886063", "gc_percent": "71.500000", "replicon_count": "0", "scaffold_count": "658", "contig_count": "658", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004349235.1-RS_2024_04_19", "annotation_date": "2024-04-19", "total_gene_count": "9555", "protein_coding_gene_count": "9257", "non_coding_gene_count": "86", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-13", "dateModified": "2019-03-13", "datePublished": "2019-03-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomadura darangshiensis" ], "sample_taxid": [ "705336" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jeju" ], "sample_host_location_id": [], "data_size": "2.677 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "9886063", "Number of Sequences": "658", "Longest Sequences (bp)": "119264", "N50 (bp)": "25974", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.7", "Number of CDSs": "8945", "Average Protein Length": "313.7", "Coding Ratio (%)": "85.1", "Number of rRNAs": "7", "Number of tRNAs": "93", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomadura darangshiensis", "strain": "strain=DSM 45941", "accession": "GCA_004349235.1", "taxid": 705336, "species_taxid": 705336, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2944, "total_fragments": 2971, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomadura madurae", "strain": "strain=DSM 43067", "accession": "GCA_900115095.1", "taxid": 1993, "species_taxid": 1993, "relation_to_type": "type", "validated": true, "ani": 88.5133, "matched_fragments": 2098, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura citrea", "strain": "strain=DSM 43461", "accession": "GCA_013409045.1", "taxid": 46158, "species_taxid": 46158, "relation_to_type": "type", "validated": true, "ani": 87.9728, "matched_fragments": 2023, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura citrea", "strain": "strain=JCM 3295", "accession": "GCA_014648455.1", "taxid": 46158, "species_taxid": 46158, "relation_to_type": "type", "validated": true, "ani": 87.9591, "matched_fragments": 1985, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura mexicana", "strain": "strain=DSM 44485", "accession": "GCA_900188105.1", "taxid": 134959, "species_taxid": 134959, "relation_to_type": "type", "validated": true, "ani": 87.891, "matched_fragments": 1922, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura coerulea", "strain": "strain=JCM 3320", "accession": "GCA_014648535.1", "taxid": 46159, "species_taxid": 46159, "relation_to_type": "type", "validated": true, "ani": 87.83, "matched_fragments": 1870, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura coerulea", "strain": "strain=DSM 43675", "accession": "GCA_014208105.1", "taxid": 46159, "species_taxid": 46159, "relation_to_type": "type", "validated": true, "ani": 87.8211, "matched_fragments": 1884, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura latina", "strain": "strain=ATCC BAA-277", "accession": "GCA_012396395.1", "taxid": 163603, "species_taxid": 163603, "relation_to_type": "type", "validated": true, "ani": 87.7695, "matched_fragments": 1832, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura latina", "strain": "strain=NBRC 106108", "accession": "GCA_001552195.1", "taxid": 163603, "species_taxid": 163603, "relation_to_type": "type", "validated": true, "ani": 87.7386, "matched_fragments": 1858, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura bangladeshensis", "strain": "strain=DSM 45347", "accession": "GCA_004348335.1", "taxid": 453573, "species_taxid": 453573, "relation_to_type": "type", "validated": true, "ani": 87.6233, "matched_fragments": 1757, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura geliboluensis", "strain": "strain=A8036", "accession": "GCA_005889745.1", "taxid": 882440, "species_taxid": 882440, "relation_to_type": "type", "validated": true, "ani": 87.1255, "matched_fragments": 1735, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura formosensis", "strain": "strain=NBRC 14204", "accession": "GCA_001552155.1", "taxid": 60706, "species_taxid": 60706, "relation_to_type": "type", "validated": true, "ani": 87.0546, "matched_fragments": 1481, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura meyerae", "strain": "strain=DSM 44715", "accession": "GCA_900188445.1", "taxid": 240840, "species_taxid": 240840, "relation_to_type": "type", "validated": true, "ani": 86.9972, "matched_fragments": 1932, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura violacea", "strain": "strain=LCR2-06", "accession": "GCA_017573465.1", "taxid": 2819934, "species_taxid": 2819934, "relation_to_type": "type", "validated": true, "ani": 85.0608, "matched_fragments": 1990, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura spongiicola", "strain": "strain=LHW52907", "accession": "GCA_003432485.1", "taxid": 2303421, "species_taxid": 2303421, "relation_to_type": "type", "validated": true, "ani": 84.5404, "matched_fragments": 1497, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura graeca", "strain": "strain=32-07", "accession": "GCA_019175365.1", "taxid": 2750812, "species_taxid": 2750812, "relation_to_type": "type", "validated": true, "ani": 83.8988, "matched_fragments": 1572, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura parmotrematis", "strain": "strain=PM05-2", "accession": "GCA_019458805.1", "taxid": 2864039, "species_taxid": 2864039, "relation_to_type": "type", "validated": true, "ani": 81.5115, "matched_fragments": 1465, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura rupiterrae", "strain": "strain=DSM 45251", "accession": "GCA_024172125.1", "taxid": 559627, "species_taxid": 559627, "relation_to_type": "type", "validated": true, "ani": 81.1481, "matched_fragments": 1453, "total_fragments": 2971, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004349235.1", "gtdb_species": "s__Spirillospora darangshiensis", "ani": 100.0, "matched_fragments": 2944, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_900115095.1", "gtdb_species": "s__Spirillospora madurae", "ani": 88.5272, "matched_fragments": 2096, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013409045.1", "gtdb_species": "s__Spirillospora citrea", "ani": 87.9751, "matched_fragments": 2021, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013372625.1", "gtdb_species": "s__Spirillospora sp013372625", "ani": 87.9034, "matched_fragments": 1678, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_900188105.1", "gtdb_species": "s__Spirillospora mexicana", "ani": 87.8689, "matched_fragments": 1925, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_013409365.1", "gtdb_species": "s__Spirillospora luteofluorescens", "ani": 87.8615, "matched_fragments": 2035, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_008327685.1", "gtdb_species": "s__Spirillospora sp008327685", "ani": 87.8512, "matched_fragments": 2025, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_004348335.1", "gtdb_species": "s__Spirillospora bangladeshensis", "ani": 87.6321, "matched_fragments": 1756, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_013364275.1", "gtdb_species": "s__Spirillospora sp013364275", "ani": 87.3793, "matched_fragments": 2049, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_006547145.1", "gtdb_species": "s__Spirillospora sp006547145", "ani": 87.3544, "matched_fragments": 1968, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_005889745.1", "gtdb_species": "s__Spirillospora geliboluensis", "ani": 87.1353, "matched_fragments": 1732, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_001552155.1", "gtdb_species": "s__Spirillospora formosensis", "ani": 87.034, "matched_fragments": 1482, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004348515.1", "gtdb_species": "s__Spirillospora sp004348515", "ani": 86.1818, "matched_fragments": 1636, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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_004349245.1", "gtdb_species": "s__Spirillospora sp004349245", "ani": 85.907, "matched_fragments": 1643, "total_fragments": 2971, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "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": 0.301, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 32.909, "optimum_ph": 7.142, "genome_size": 8227448.539, "gc_content": 72.459, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.833, "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": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.333, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Actinomadura", "darangshiensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }