{ "type": "genome", "identifier": "GCF_007829925.1", "organism": "Micromonospora palomenae", "title": "Micromonospora palomenae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007829925.1", "bioproject": "PRJNA224116", "biosample": "SAMN12024693", "wgs_master": "VIXA00000000.1", "refseq_category": "reference genome", "taxid": "1461247", "species_taxid": "1461247", "organism_name": "Micromonospora palomenae", "infraspecific_name": "strain=DSM 102131", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/08/02", "asm_name": "ASM782992v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_007829925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/829/925/GCF_007829925.1_ASM782992v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6655188", "genome_size_ungapped": "6655188", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007829925.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "6133", "protein_coding_gene_count": "5961", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-08-02", "dateModified": "2019-08-02", "datePublished": "2019-08-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Micromonospora palomenae" ], "sample_taxid": [ "1461247" ], "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": "1.750 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6655188", "Number of Sequences": "8", "Longest Sequences (bp)": "2477088", "N50 (bp)": "2092086", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.0", "Number of CDSs": "6182", "Average Protein Length": "319.1", "Coding Ratio (%)": "88.9", "Number of rRNAs": "12", "Number of tRNAs": "80", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Micromonospora palomenae", "strain": "strain=DSM 102131", "accession": "GCA_007829925.1", "taxid": 1461247, "species_taxid": 1461247, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2210, "total_fragments": 2215, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Micromonospora purpureochromogenes", "strain": "strain=DSM 43821", "accession": "GCA_900091515.1", "taxid": 47872, "species_taxid": 47872, "relation_to_type": "type", "validated": true, "ani": 95.9891, "matched_fragments": 1886, "total_fragments": 2215, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Micromonospora coxensis", "strain": "strain=DSM 45161", "accession": "GCA_900090295.1", "taxid": 356852, "species_taxid": 356852, "relation_to_type": "type", "validated": true, "ani": 89.2918, "matched_fragments": 1608, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora halophytica", "strain": "strain=DSM 43171", "accession": "GCA_900090245.1", "taxid": 47864, "species_taxid": 47864, "relation_to_type": "type", "validated": true, "ani": 89.1458, "matched_fragments": 1467, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora kangleipakensis", "strain": "strain=DSM 45612", "accession": "GCA_004217615.1", "taxid": 1077942, "species_taxid": 1077942, "relation_to_type": "type", "validated": true, "ani": 87.8509, "matched_fragments": 1589, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora veneta", "strain": "strain=CAP181", "accession": "GCA_016598485.1", "taxid": 2796464, "species_taxid": 2796464, "relation_to_type": "type", "validated": true, "ani": 87.5382, "matched_fragments": 1557, "total_fragments": 2215, "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": 87.4123, "matched_fragments": 1272, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora fulviviridis", "strain": "strain=JCM 3259", "accession": "GCA_014648395.1", "taxid": 47860, "species_taxid": 47860, "relation_to_type": "type", "validated": true, "ani": 87.0288, "matched_fragments": 1618, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora chersina", "strain": "strain=DSM 44151", "accession": "GCA_900091475.1", "taxid": 47854, "species_taxid": 47854, "relation_to_type": "type", "validated": true, "ani": 86.8526, "matched_fragments": 1613, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora auratinigra", "strain": "strain=DSM 44815", "accession": "GCA_900089595.1", "taxid": 261654, "species_taxid": 261654, "relation_to_type": "type", "validated": true, "ani": 86.7852, "matched_fragments": 1534, "total_fragments": 2215, "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": 86.7246, "matched_fragments": 1616, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora chaiyaphumensis", "strain": "strain=DSM 45246", "accession": "GCA_900091435.1", "taxid": 307119, "species_taxid": 307119, "relation_to_type": "type", "validated": true, "ani": 86.7155, "matched_fragments": 1597, "total_fragments": 2215, "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": 86.6799, "matched_fragments": 1457, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora viridifaciens", "strain": "strain=DSM 43909", "accession": "GCA_900091545.1", "taxid": 1881, "species_taxid": 1881, "relation_to_type": "type", "validated": true, "ani": 86.3212, "matched_fragments": 1420, "total_fragments": 2215, "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": 86.147, "matched_fragments": 1331, "total_fragments": 2215, "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": 86.1424, "matched_fragments": 1454, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora eburnea", "strain": "strain=DSM 44814", "accession": "GCA_900090225.1", "taxid": 227316, "species_taxid": 227316, "relation_to_type": "type", "validated": true, "ani": 85.9482, "matched_fragments": 1399, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora haikouensis", "strain": "strain=DSM 45626", "accession": "GCA_900091595.1", "taxid": 686309, "species_taxid": 686309, "relation_to_type": "type", "validated": true, "ani": 85.9433, "matched_fragments": 1403, "total_fragments": 2215, "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": 84.1359, "matched_fragments": 1337, "total_fragments": 2215, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_900091515.1", "gtdb_species": "s__Micromonospora purpureochromogenes", "ani": 95.9728, "matched_fragments": 1886, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.27", "min_intra_species_ani": "95.68", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_900090295.1", "gtdb_species": "s__Micromonospora coxensis", "ani": 89.2735, "matched_fragments": 1613, "total_fragments": 2215, "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_900090245.1", "gtdb_species": "s__Micromonospora halophytica", "ani": 89.0904, "matched_fragments": 1473, "total_fragments": 2215, "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_004217615.1", "gtdb_species": "s__Micromonospora kangleipakensis", "ani": 87.8644, "matched_fragments": 1586, "total_fragments": 2215, "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_003172935.1", "gtdb_species": "s__Micromonospora sp003172935", "ani": 87.5492, "matched_fragments": 1450, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004348595.1", "gtdb_species": "s__Micromonospora sp004348595", "ani": 87.5359, "matched_fragments": 1252, "total_fragments": 2215, "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_016598485.1", "gtdb_species": "s__Micromonospora veneta", "ani": 87.5027, "matched_fragments": 1561, "total_fragments": 2215, "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_004348325.1", "gtdb_species": "s__Micromonospora sp004348325", "ani": 87.045, "matched_fragments": 1216, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.89", "min_intra_species_ani": "97.89", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014648395.1", "gtdb_species": "s__Micromonospora fulviviridis", "ani": 87.0184, "matched_fragments": 1619, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.01", "min_intra_species_ani": "95.01", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.74", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008868175.1", "gtdb_species": "s__Micromonospora sp008868175", "ani": 86.9292, "matched_fragments": 1442, "total_fragments": 2215, "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_900091475.1", "gtdb_species": "s__Micromonospora chersina", "ani": 86.8426, "matched_fragments": 1614, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.87", "min_intra_species_ani": "95.82", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900089595.1", "gtdb_species": "s__Micromonospora auratinigra", "ani": 86.8422, "matched_fragments": 1531, "total_fragments": 2215, "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_900091435.1", "gtdb_species": "s__Micromonospora chaiyaphumensis", "ani": 86.7429, "matched_fragments": 1593, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.16", "min_intra_species_ani": "95.15", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900090235.1", "gtdb_species": "s__Micromonospora echinaurantiaca", "ani": 86.7387, "matched_fragments": 1617, "total_fragments": 2215, "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_900090265.1", "gtdb_species": "s__Micromonospora rifamycinica", "ani": 86.6819, "matched_fragments": 1413, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "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_000982955.1", "gtdb_species": "s__Micromonospora sp000982955", "ani": 86.3357, "matched_fragments": 1437, "total_fragments": 2215, "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_900091545.1", "gtdb_species": "s__Micromonospora viridifaciens", "ani": 86.3334, "matched_fragments": 1420, "total_fragments": 2215, "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_014205165.1", "gtdb_species": "s__Micromonospora carbonacea", "ani": 85.9723, "matched_fragments": 1434, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.5545, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900091595.1", "gtdb_species": "s__Micromonospora haikouensis", "ani": 85.9525, "matched_fragments": 1401, "total_fragments": 2215, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.5545, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.244, "cell_length": 0.698, "doubling_h": null, "growth_tmp": 28.0, "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", "palomenae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }