{ "type": "genome", "identifier": "GCF_003626655.1", "organism": "Micromonospora costi", "title": "Micromonospora costi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Japan Collection of Microorganisms, Microbe Division, RIKEN BioResources Center, Tsukuba, Japan", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003626655.1", "bioproject": "PRJNA224116", "biosample": "SAMN10141428", "wgs_master": "RBAN00000000.1", "refseq_category": "reference genome", "taxid": "1530042", "species_taxid": "1530042", "organism_name": "Micromonospora costi", "infraspecific_name": "strain=CS1-12", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/07", "asm_name": "ASM362665v1", "asm_submitter": "Japan Collection of Microorganisms, Microbe Division, RIKEN BioResources Center, Tsukuba, Japan", "gbrs_paired_asm": "GCA_003626655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/626/655/GCF_003626655.1_ASM362665v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7182425", "genome_size_ungapped": "7182425", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003626655.1-RS_2024_04_03", "annotation_date": "2024-04-03", "total_gene_count": "6653", "protein_coding_gene_count": "6469", "non_coding_gene_count": "95", "pubmed_id": "25687348" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-07", "dateModified": "2018-10-07", "datePublished": "2018-10-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Micromonospora costi" ], "sample_taxid": [ "1530042" ], "sample_host_organism": [ "Hellenia speciosa" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "1.899 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)": "7182425", "Number of Sequences": "20", "Longest Sequences (bp)": "2378827", "N50 (bp)": "1122969", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.0", "Number of CDSs": "6649", "Average Protein Length": "321.7", "Coding Ratio (%)": "89.3", "Number of rRNAs": "4", "Number of tRNAs": "97", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Micromonospora costi", "strain": "strain=CS1-12", "accession": "GCA_003626655.1", "taxid": 1530042, "species_taxid": 1530042, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2384, "total_fragments": 2385, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Micromonospora globbae", "strain": "strain=WPS1-2", "accession": "GCA_003610785.1", "taxid": 1894969, "species_taxid": 1894969, "relation_to_type": "type", "validated": true, "ani": 87.6142, "matched_fragments": 1794, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora musae", "strain": "strain=MS1-9", "accession": "GCA_003626635.1", "taxid": 1894970, "species_taxid": 1894970, "relation_to_type": "type", "validated": true, "ani": 86.8269, "matched_fragments": 1771, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora avicenniae", "strain": "strain=DSM 45758", "accession": "GCA_900156065.1", "taxid": 1198245, "species_taxid": 1198245, "relation_to_type": "type", "validated": true, "ani": 86.7896, "matched_fragments": 1730, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora krabiensis", "strain": "strain=DSM 45344", "accession": "GCA_900091425.1", "taxid": 307121, "species_taxid": 307121, "relation_to_type": "type", "validated": true, "ani": 86.7237, "matched_fragments": 1714, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora echinaurantiaca", "strain": "strain=DSM 43904", "accession": "GCA_900090235.1", "taxid": 47857, "species_taxid": 47857, "relation_to_type": "type", "validated": true, "ani": 85.9241, "matched_fragments": 1677, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora deserti", "strain": "strain=13K206", "accession": "GCA_003236335.1", "taxid": 2070366, "species_taxid": 2070366, "relation_to_type": "type", "validated": true, "ani": 85.3625, "matched_fragments": 1238, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora phytophila", "strain": "strain=DSM 105363", "accession": "GCA_023656545.1", "taxid": 709888, "species_taxid": 709888, "relation_to_type": "type", "validated": true, "ani": 85.3008, "matched_fragments": 1198, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora acroterricola", "strain": "strain=5R2A7", "accession": "GCA_003172955.1", "taxid": 2202421, "species_taxid": 2202421, "relation_to_type": "type", "validated": true, "ani": 85.2847, "matched_fragments": 1449, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora cremea", "strain": "strain=DSM 45599", "accession": "GCA_900143515.1", "taxid": 709881, "species_taxid": 709881, "relation_to_type": "type", "validated": true, "ani": 85.1576, "matched_fragments": 1697, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora palomenae", "strain": "strain=DSM 102131", "accession": "GCA_007829925.1", "taxid": 1461247, "species_taxid": 1461247, "relation_to_type": "type", "validated": true, "ani": 84.9648, "matched_fragments": 1513, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora coxensis", "strain": "strain=DSM 45161", "accession": "GCA_900090295.1", "taxid": 356852, "species_taxid": 356852, "relation_to_type": "type", "validated": true, "ani": 84.522, "matched_fragments": 1480, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora ferruginea", "strain": "strain=28ISP2-46", "accession": "GCA_013694245.1", "taxid": 2749844, "species_taxid": 2749844, "relation_to_type": "type", "validated": true, "ani": 83.9782, "matched_fragments": 1423, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora humida", "strain": "strain=MMS20-R1-14", "accession": "GCA_016901255.1", "taxid": 2809018, "species_taxid": 2809018, "relation_to_type": "type", "validated": true, "ani": 83.4983, "matched_fragments": 1370, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora radicis", "strain": "strain=AZ1-13", "accession": "GCA_003583405.1", "taxid": 1894971, "species_taxid": 1894971, "relation_to_type": "type", "validated": true, "ani": 83.3138, "matched_fragments": 1246, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora phaseoli", "strain": "strain=NBRC 110907", "accession": "GCA_016863675.1", "taxid": 1144548, "species_taxid": 1144548, "relation_to_type": "type", "validated": true, "ani": 83.0914, "matched_fragments": 1289, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora pattaloongensis", "strain": "strain=DSM 45245", "accession": "GCA_900107255.1", "taxid": 405436, "species_taxid": 405436, "relation_to_type": "type", "validated": true, "ani": 81.197, "matched_fragments": 1072, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinoplanes capillaceus", "strain": "strain=NBRC 16408", "accession": "GCA_016862055.1", "taxid": 76756, "species_taxid": 76756, "relation_to_type": "type", "validated": true, "ani": 78.6204, "matched_fragments": 1050, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinoplanes flavus", "strain": "strain=NEAU-H7", "accession": "GCA_017592555.1", "taxid": 2820290, "species_taxid": 2820290, "relation_to_type": "type", "validated": true, "ani": 78.5448, "matched_fragments": 1054, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinoplanes rishiriensis", "strain": "strain=NBRC 108556", "accession": "GCA_016862375.1", "taxid": 1050105, "species_taxid": 1050105, "relation_to_type": "type", "validated": true, "ani": 78.5132, "matched_fragments": 1096, "total_fragments": 2385, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003626655.1", "gtdb_species": "s__Micromonospora costi", "ani": 100.0, "matched_fragments": 2384, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_003610785.1", "gtdb_species": "s__Micromonospora globbae", "ani": 87.6033, "matched_fragments": 1796, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_004348525.1", "gtdb_species": "s__Micromonospora sp004348525", "ani": 86.9352, "matched_fragments": 1581, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_003626635.1", "gtdb_species": "s__Micromonospora musae", "ani": 86.8322, "matched_fragments": 1770, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.26", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900156065.1", "gtdb_species": "s__Micromonospora avicenniae", "ani": 86.7586, "matched_fragments": 1736, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_900091425.1", "gtdb_species": "s__Micromonospora krabiensis", "ani": 86.7318, "matched_fragments": 1713, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_900090235.1", "gtdb_species": "s__Micromonospora echinaurantiaca", "ani": 85.8957, "matched_fragments": 1684, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003236335.1", "gtdb_species": "s__Micromonospora deserti", "ani": 85.3154, "matched_fragments": 1243, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_003172955.1", "gtdb_species": "s__Micromonospora sp003172955", "ani": 85.3144, "matched_fragments": 1445, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_900143515.1", "gtdb_species": "s__Micromonospora cremea", "ani": 85.1747, "matched_fragments": 1693, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_900090295.1", "gtdb_species": "s__Micromonospora coxensis", "ani": 84.5425, "matched_fragments": 1477, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_016863555.1", "gtdb_species": "s__Micromonospora qiuiae", "ani": 82.9113, "matched_fragments": 1199, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_900107255.1", "gtdb_species": "s__Micromonospora_E pattaloongensis", "ani": 81.1767, "matched_fragments": 1076, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E", "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_017592555.1", "gtdb_species": "s__Actinoplanes sp017592555", "ani": 78.5747, "matched_fragments": 1044, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes", "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_016862375.1", "gtdb_species": "s__Actinoplanes rishiriensis", "ani": 78.5241, "matched_fragments": 1095, "total_fragments": 2385, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes", "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": -0.244, "cell_length": 0.698, "doubling_h": null, "growth_tmp": 27.687, "optimum_tmp": 29.972, "optimum_ph": 7.268, "genome_size": 6974886.426, "gc_content": 72.396, "coding_genes": 6227.25, "rRNA16S_genes": 3.0, "tRNA_genes": 51.0, "gram_stain": 1.0, "sporulation": 1.0, "motility": 0.0, "range_salinity": 0.0, "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": 0.2, "coccus_cell_shape": 0.4, "filament_cell_shape": 0.4, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Micromonospora", "costi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }