{ "type": "genome", "identifier": "GCF_900089585.1", "organism": "Micromonospora sediminicola", "title": "Micromonospora sediminicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900089585.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488363", "wgs_master": "FLRH00000000.1", "refseq_category": "reference genome", "taxid": "946078", "species_taxid": "946078", "organism_name": "Micromonospora sediminicola", "infraspecific_name": "strain=DSM 45794", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/06/17", "asm_name": "IMG-taxon 2622736535 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900089585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/089/585/GCF_900089585.1_IMG-taxon_2622736535_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6885700", "genome_size_ungapped": "6885700", "gc_percent": "73.500000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900089585.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "6446", "protein_coding_gene_count": "6297", "non_coding_gene_count": "82", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-06-17", "dateModified": "2016-06-17", "datePublished": "2016-06-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Micromonospora sediminicola" ], "sample_taxid": [ "946078" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.791 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)": "6885700", "Number of Sequences": "5", "Longest Sequences (bp)": "4643122", "N50 (bp)": "4643122", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.6", "Number of CDSs": "6466", "Average Protein Length": "321.8", "Coding Ratio (%)": "90.6", "Number of rRNAs": "9", "Number of tRNAs": "89", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Micromonospora sediminicola", "strain": "strain=DSM 45794", "accession": "GCA_900089585.1", "taxid": 946078, "species_taxid": 946078, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2287, "total_fragments": 2293, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Micromonospora maritima", "strain": "", "accession": "GCA_902825405.1", "taxid": 986711, "species_taxid": 986711, "relation_to_type": "type", "validated": true, "ani": 94.5378, "matched_fragments": 1346, "total_fragments": 2293, "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": 90.9795, "matched_fragments": 1792, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora humi", "strain": "strain=DSM 45647", "accession": "GCA_900090105.1", "taxid": 745366, "species_taxid": 745366, "relation_to_type": "type", "validated": true, "ani": 90.7565, "matched_fragments": 1753, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora aurantiaca", "strain": "strain=ATCC 27029", "accession": "GCA_000145235.1", "taxid": 47850, "species_taxid": 47850, "relation_to_type": "type", "validated": true, "ani": 89.9524, "matched_fragments": 1737, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora aurantiaca", "strain": "strain=ATCC 27029", "accession": "GCA_003721415.1", "taxid": 47850, "species_taxid": 47850, "relation_to_type": "type", "validated": true, "ani": 89.9291, "matched_fragments": 1703, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora chalcea", "strain": "strain=DSM 43026", "accession": "GCA_002926165.1", "taxid": 1874, "species_taxid": 1874, "relation_to_type": "type", "validated": true, "ani": 89.8494, "matched_fragments": 1599, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora terminaliae", "strain": "strain=TMS7", "accession": "GCA_010671825.1", "taxid": 1914461, "species_taxid": 1914461, "relation_to_type": "type", "validated": true, "ani": 88.358, "matched_fragments": 1592, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora narathiwatensis", "strain": "strain=DSM 45248", "accession": "GCA_900089605.1", "taxid": 299146, "species_taxid": 299146, "relation_to_type": "type", "validated": true, "ani": 87.0073, "matched_fragments": 1502, "total_fragments": 2293, "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": 86.7284, "matched_fragments": 1437, "total_fragments": 2293, "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": 86.5488, "matched_fragments": 1465, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora mirobrigensis", "strain": "strain=DSM 44830", "accession": "GCA_900091555.1", "taxid": 262898, "species_taxid": 262898, "relation_to_type": "type", "validated": true, "ani": 86.1122, "matched_fragments": 1511, "total_fragments": 2293, "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": 86.0825, "matched_fragments": 1589, "total_fragments": 2293, "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": 85.6639, "matched_fragments": 1476, "total_fragments": 2293, "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": 85.3875, "matched_fragments": 1130, "total_fragments": 2293, "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": 84.8704, "matched_fragments": 1468, "total_fragments": 2293, "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": 84.7634, "matched_fragments": 1296, "total_fragments": 2293, "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": 83.5539, "matched_fragments": 1310, "total_fragments": 2293, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900089585.1", "gtdb_species": "s__Micromonospora sediminicola", "ani": 100.0, "matched_fragments": 2285, "total_fragments": 2293, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_902825405.1", "gtdb_species": "s__Micromonospora maritima", "ani": 94.5666, "matched_fragments": 1344, "total_fragments": 2293, "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_013694245.1", "gtdb_species": "s__Micromonospora sp013694245", "ani": 90.9346, "matched_fragments": 1796, "total_fragments": 2293, "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_900090105.1", "gtdb_species": "s__Micromonospora humi", "ani": 90.7435, "matched_fragments": 1754, "total_fragments": 2293, "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_003027925.1", "gtdb_species": "s__Micromonospora sp003027925", "ani": 90.6386, "matched_fragments": 1719, "total_fragments": 2293, "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_002140155.1", "gtdb_species": "s__Micromonospora sp002140155", "ani": 90.3236, "matched_fragments": 1624, "total_fragments": 2293, "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_900091605.1", "gtdb_species": "s__Micromonospora tulbaghiae", "ani": 90.0351, "matched_fragments": 1673, "total_fragments": 2293, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.1942, "mean_intra_species_ani": "97.73", "min_intra_species_ani": "96.20", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000145235.1", "gtdb_species": "s__Micromonospora aurantiaca", "ani": 89.984, "matched_fragments": 1734, "total_fragments": 2293, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.1942, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "95.58", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.84", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_002926165.1", "gtdb_species": "s__Micromonospora chalcea", "ani": 89.8041, "matched_fragments": 1603, "total_fragments": 2293, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_008868175.1", "gtdb_species": "s__Micromonospora sp008868175", "ani": 88.4868, "matched_fragments": 1488, "total_fragments": 2293, "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_000982955.1", "gtdb_species": "s__Micromonospora sp000982955", "ani": 87.3835, "matched_fragments": 1497, "total_fragments": 2293, "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_900089605.1", "gtdb_species": "s__Micromonospora narathiwatensis", "ani": 87.0113, "matched_fragments": 1502, "total_fragments": 2293, "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_900091555.1", "gtdb_species": "s__Micromonospora mirobrigensis", "ani": 86.0608, "matched_fragments": 1518, "total_fragments": 2293, "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": 86.0559, "matched_fragments": 1593, "total_fragments": 2293, "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": 85.6908, "matched_fragments": 1472, "total_fragments": 2293, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.244, "cell_length": 0.698, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 31.0, "optimum_ph": 9.0, "genome_size": 6885700.0, "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": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Micromonospora", "sediminicola" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }