{ "type": "genome", "identifier": "GCF_006716765.1", "organism": "Actinomadura hallensis", "title": "Actinomadura hallensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006716765.1", "bioproject": "PRJNA224116", "biosample": "SAMN12024936", "wgs_master": "VFPO00000000.1", "refseq_category": "reference genome", "taxid": "337895", "species_taxid": "337895", "organism_name": "Actinomadura hallensis", "infraspecific_name": "strain=DSM 45043", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/08", "asm_name": "ASM671676v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_006716765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/716/765/GCF_006716765.1_ASM671676v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6701511", "genome_size_ungapped": "6701511", "gc_percent": "72.500000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006716765.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "6134", "protein_coding_gene_count": "5989", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-08", "dateModified": "2019-07-08", "datePublished": "2019-07-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomadura hallensis" ], "sample_taxid": [ "337895" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.779 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)": "6701511", "Number of Sequences": "1", "Longest Sequences (bp)": "6701511", "N50 (bp)": "6701511", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.6", "Number of CDSs": "6173", "Average Protein Length": "319.9", "Coding Ratio (%)": "88.4", "Number of rRNAs": "16", "Number of tRNAs": "82", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomadura hallensis", "strain": "strain=DSM 45043", "accession": "GCA_006716765.1", "taxid": 337895, "species_taxid": 337895, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2232, "total_fragments": 2233, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomadura bangladeshensis", "strain": "strain=DSM 45347", "accession": "GCA_004348335.1", "taxid": 453573, "species_taxid": 453573, "relation_to_type": "type", "validated": true, "ani": 85.9383, "matched_fragments": 1527, "total_fragments": 2233, "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": 85.8755, "matched_fragments": 1630, "total_fragments": 2233, "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": 85.8003, "matched_fragments": 1685, "total_fragments": 2233, "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": 85.797, "matched_fragments": 1652, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura madurae", "strain": "strain=DSM 43067", "accession": "GCA_900115095.1", "taxid": 1993, "species_taxid": 1993, "relation_to_type": "type", "validated": true, "ani": 85.7368, "matched_fragments": 1703, "total_fragments": 2233, "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": 85.6728, "matched_fragments": 1379, "total_fragments": 2233, "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": 85.5569, "matched_fragments": 1460, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura soli", "strain": "strain=14C53", "accession": "GCA_005889715.1", "taxid": 2508997, "species_taxid": 2508997, "relation_to_type": "type", "validated": true, "ani": 85.3681, "matched_fragments": 1400, "total_fragments": 2233, "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": 85.3393, "matched_fragments": 1640, "total_fragments": 2233, "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": 85.2461, "matched_fragments": 1594, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura syzygii", "strain": "strain=GKU157", "accession": "GCA_008085905.1", "taxid": 1427538, "species_taxid": 1427538, "relation_to_type": "type", "validated": true, "ani": 84.641, "matched_fragments": 1577, "total_fragments": 2233, "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": 84.4046, "matched_fragments": 1400, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura montaniterrae", "strain": "strain=CYP1-1B", "accession": "GCA_008923365.1", "taxid": 1803903, "species_taxid": 1803903, "relation_to_type": "type", "validated": true, "ani": 84.1948, "matched_fragments": 1503, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinomadura physcomitrii", "strain": "strain=LD22", "accession": "GCA_008923205.2", "taxid": 2650748, "species_taxid": 2650748, "relation_to_type": "type", "validated": true, "ani": 84.1879, "matched_fragments": 1558, "total_fragments": 2233, "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": 84.0433, "matched_fragments": 1620, "total_fragments": 2233, "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": 83.5684, "matched_fragments": 1442, "total_fragments": 2233, "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": 81.5246, "matched_fragments": 1319, "total_fragments": 2233, "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": 81.1264, "matched_fragments": 1277, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermomonospora curvata", "strain": "strain=DSM 43183", "accession": "GCA_000024385.1", "taxid": 2020, "species_taxid": 2020, "relation_to_type": "type", "validated": true, "ani": 80.0249, "matched_fragments": 1015, "total_fragments": 2233, "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": 77.2224, "matched_fragments": 770, "total_fragments": 2233, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006716765.1", "gtdb_species": "s__Spirillospora hallensis", "ani": 100.0, "matched_fragments": 2233, "total_fragments": 2233, "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_014648675.1", "gtdb_species": "s__Spirillospora livida", "ani": 89.1526, "matched_fragments": 1839, "total_fragments": 2233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "97.09", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004349245.1", "gtdb_species": "s__Spirillospora sp004349245", "ani": 88.9498, "matched_fragments": 1735, "total_fragments": 2233, "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_004348665.1", "gtdb_species": "s__Spirillospora sp004348665", "ani": 88.6792, "matched_fragments": 1549, "total_fragments": 2233, "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_004348515.1", "gtdb_species": "s__Spirillospora sp004348515", "ani": 87.4033, "matched_fragments": 1562, "total_fragments": 2233, "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_001552195.1", "gtdb_species": "s__Spirillospora latina", "ani": 85.8116, "matched_fragments": 1651, "total_fragments": 2233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001552155.1", "gtdb_species": "s__Spirillospora formosensis", "ani": 85.6455, "matched_fragments": 1382, "total_fragments": 2233, "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_005889745.1", "gtdb_species": "s__Spirillospora geliboluensis", "ani": 85.5016, "matched_fragments": 1468, "total_fragments": 2233, "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": 85.2504, "matched_fragments": 1648, "total_fragments": 2233, "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_008085905.1", "gtdb_species": "s__Spirillospora syzygii", "ani": 84.5865, "matched_fragments": 1586, "total_fragments": 2233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.88", "min_intra_species_ani": "95.88", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008923365.1", "gtdb_species": "s__Spirillospora montaniterrae", "ani": 84.1835, "matched_fragments": 1505, "total_fragments": 2233, "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_008923205.2", "gtdb_species": "s__Spirillospora physcomitrii", "ani": 84.1353, "matched_fragments": 1566, "total_fragments": 2233, "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_000024385.1", "gtdb_species": "s__Thermomonospora curvata", "ani": 80.0383, "matched_fragments": 1017, "total_fragments": 2233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermomonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.63", "min_intra_species_ani": "99.63", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018476525.1", "gtdb_species": "s__Acrocarpospora sp018476525", "ani": 77.2292, "matched_fragments": 762, "total_fragments": 2233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora", "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_009687885.1", "gtdb_species": "s__Acrocarpospora pleiomorpha", "ani": 77.1907, "matched_fragments": 748, "total_fragments": 2233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora", "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": 32.5, "optimum_ph": 7.0, "genome_size": 8227448.539, "gc_content": 72.459, "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": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Actinomadura", "hallensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }