{ "type": "genome", "identifier": "GCF_003583405.1", "organism": "Micromonospora radicis", "title": "Micromonospora radicis", "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_003583405.1", "bioproject": "PRJNA224116", "biosample": "SAMN09939698", "wgs_master": "QXEC00000000.1", "refseq_category": "reference genome", "taxid": "1894971", "species_taxid": "1894971", "organism_name": "Micromonospora radicis", "infraspecific_name": "strain=AZ1-13", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/09/20", "asm_name": "CHULA_Jazt_1.1 for version 1.1 of the Jishengella sp. nov. AZ1-13 genome from a lab in CHULA", "asm_submitter": "Japan Collection of Microorganisms, Microbe Division, RIKEN BioResources Center, Tsukuba, Japan", "gbrs_paired_asm": "GCA_003583405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/583/405/GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5963223", "genome_size_ungapped": "5963223", "gc_percent": "72.000000", "replicon_count": "0", "scaffold_count": "83", "contig_count": "83", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003583405.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "5398", "protein_coding_gene_count": "5240", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-09-20", "dateModified": "2018-09-20", "datePublished": "2018-09-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Micromonospora radicis" ], "sample_taxid": [ "1894971" ], "sample_host_organism": [ "Azadirachta indica A. Juss. var. siamensis Valenton" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "1.587 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)": "5963223", "Number of Sequences": "83", "Longest Sequences (bp)": "562353", "N50 (bp)": "205084", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.9", "Number of CDSs": "5344", "Average Protein Length": "330.7", "Coding Ratio (%)": "88.9", "Number of rRNAs": "2", "Number of tRNAs": "73", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Micromonospora radicis", "strain": "strain=AZ1-13", "accession": "GCA_003583405.1", "taxid": 1894971, "species_taxid": 1894971, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1953, "total_fragments": 1956, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Micromonospora zingiberis", "strain": "strain=PLAI 1-1", "accession": "GCA_004331455.1", "taxid": 2053011, "species_taxid": 2053011, "relation_to_type": "type", "validated": true, "ani": 89.1462, "matched_fragments": 1547, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora maris", "strain": "strain=NRRL B-24793", "accession": "GCA_001507315.1", "taxid": 1003110, "species_taxid": 1003110, "relation_to_type": "type", "validated": true, "ani": 88.1116, "matched_fragments": 1460, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora fiedleri", "strain": "strain=MG-37", "accession": "GCA_016774385.1", "taxid": 1157498, "species_taxid": 1157498, "relation_to_type": "type", "validated": true, "ani": 88.0229, "matched_fragments": 1502, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora gifhornensis", "strain": "strain=NBRC 16317", "accession": "GCA_016863515.1", "taxid": 84594, "species_taxid": 84594, "relation_to_type": "type", "validated": true, "ani": 88.0133, "matched_fragments": 1478, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora maris", "strain": "strain=AB-18-032", "accession": "GCA_000204155.1", "taxid": 1003110, "species_taxid": 1003110, "relation_to_type": "type", "validated": true, "ani": 88.0001, "matched_fragments": 1473, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora craterilacus", "strain": "strain=NA12", "accession": "GCA_003236315.1", "taxid": 1655439, "species_taxid": 1655439, "relation_to_type": "type", "validated": true, "ani": 87.9551, "matched_fragments": 1320, "total_fragments": 1956, "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": 87.0623, "matched_fragments": 1420, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora craniellae", "strain": "strain=LHW63014", "accession": "GCA_003419945.1", "taxid": 2294034, "species_taxid": 2294034, "relation_to_type": "type", "validated": true, "ani": 87.0212, "matched_fragments": 1335, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora craniellae", "strain": "strain=LHW63014", "accession": "GCA_014764405.1", "taxid": 2294034, "species_taxid": 2294034, "relation_to_type": "type", "validated": true, "ani": 86.9318, "matched_fragments": 1356, "total_fragments": 1956, "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": 84.9243, "matched_fragments": 979, "total_fragments": 1956, "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": 84.6258, "matched_fragments": 1084, "total_fragments": 1956, "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": 84.0844, "matched_fragments": 1099, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora carbonacea", "strain": "strain=aurantiaca", "accession": "GCA_013389765.1", "taxid": 47853, "species_taxid": 47853, "relation_to_type": "type", "validated": true, "ani": 83.9435, "matched_fragments": 1311, "total_fragments": 1956, "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": 83.8638, "matched_fragments": 1293, "total_fragments": 1956, "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": 83.8056, "matched_fragments": 1156, "total_fragments": 1956, "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": 83.7229, "matched_fragments": 1242, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Micromonospora inaquosa", "strain": "strain=LB39", "accession": "GCA_003857055.1", "taxid": 2203716, "species_taxid": 2203716, "relation_to_type": "type", "validated": true, "ani": 83.5075, "matched_fragments": 1141, "total_fragments": 1956, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003583405.1", "gtdb_species": "s__Micromonospora radicis", "ani": 100.0, "matched_fragments": 1953, "total_fragments": 1956, "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_004331455.1", "gtdb_species": "s__Micromonospora zingiberis", "ani": 89.1599, "matched_fragments": 1545, "total_fragments": 1956, "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_016863515.1", "gtdb_species": "s__Micromonospora gifhornensis", "ani": 88.0372, "matched_fragments": 1475, "total_fragments": 1956, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.77", "min_intra_species_ani": "95.90", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003236315.1", "gtdb_species": "s__Micromonospora craterilacus", "ani": 87.9321, "matched_fragments": 1322, "total_fragments": 1956, "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": "GCA_005402585.1", "gtdb_species": "s__Micromonospora sp005402585", "ani": 87.7573, "matched_fragments": 1453, "total_fragments": 1956, "gtdb_taxonomy": 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