{ "type": "genome", "identifier": "GCF_014208105.1", "organism": "Actinomadura coerulea", "title": "Actinomadura coerulea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014208105.1", "bioproject": "PRJNA224116", "biosample": "SAMN05878273", "wgs_master": "JACHMQ000000000.1", "refseq_category": "reference genome", "taxid": "46159", "species_taxid": "46159", "organism_name": "Actinomadura coerulea", "infraspecific_name": "strain=DSM 43675", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1420810v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014208105.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/208/105/GCF_014208105.1_ASM1420810v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8190213", "genome_size_ungapped": "8190213", "gc_percent": "72.500000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014208105.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "7645", "protein_coding_gene_count": "7501", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Actinomadura coerulea" ], "sample_taxid": [ "46159" ], "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": "2.178 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 10.65, "strain_heterogeneity": 57.14, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "8190213", "Number of Sequences": "1", "Longest Sequences (bp)": "8190213", "N50 (bp)": "8190213", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.6", "Number of CDSs": "7710", "Average Protein Length": "317.3", "Coding Ratio (%)": "89.6", "Number of rRNAs": "15", "Number of tRNAs": "92", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Actinomadura coerulea", "strain": "strain=DSM 43675", "accession": "GCA_014208105.1", "taxid": 46159, "species_taxid": 46159, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2727, "total_fragments": 2730, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomadura coerulea", "strain": "strain=JCM 3320", "accession": "GCA_014648535.1", "taxid": 46159, "species_taxid": 46159, "relation_to_type": "type", "validated": true, "ani": 99.9866, "matched_fragments": 2673, "total_fragments": 2730, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Actinomadura citrea", "strain": "strain=JCM 3295", "accession": "GCA_014648455.1", "taxid": 46158, "species_taxid": 46158, "relation_to_type": "type", "validated": true, "ani": 93.7126, "matched_fragments": 2371, "total_fragments": 2730, "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": 93.6737, "matched_fragments": 2417, "total_fragments": 2730, "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": 93.5817, "matched_fragments": 2284, "total_fragments": 2730, "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": 84.9188, "matched_fragments": 1970, "total_fragments": 2730, "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": 84.3593, "matched_fragments": 1533, "total_fragments": 2730, "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": 84.1801, "matched_fragments": 1671, "total_fragments": 2730, "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": 81.8203, "matched_fragments": 1508, "total_fragments": 2730, "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": 81.5029, "matched_fragments": 1473, "total_fragments": 2730, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 10.65, "strain_heterogeneity": 57.14 }, "gtdb_result": [ { "accession": "GCF_014208105.1", "gtdb_species": "s__Spirillospora coerulea", "ani": 100.0, "matched_fragments": 2728, "total_fragments": 2730, "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": "conclusive" }, { "accession": "GCF_013409045.1", "gtdb_species": "s__Spirillospora citrea", "ani": 93.6928, "matched_fragments": 2413, "total_fragments": 2730, "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_900188105.1", "gtdb_species": "s__Spirillospora mexicana", "ani": 93.5817, "matched_fragments": 2284, "total_fragments": 2730, "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": 93.5318, "matched_fragments": 2408, "total_fragments": 2730, "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": 91.6779, "matched_fragments": 2243, "total_fragments": 2730, "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": 91.2287, "matched_fragments": 2215, "total_fragments": 2730, "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_900115095.1", "gtdb_species": "s__Spirillospora madurae", "ani": 87.6904, "matched_fragments": 2015, "total_fragments": 2730, "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": "-" } ] }, "_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", "coerulea" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }