{ "type": "genome", "identifier": "GCF_004135405.1", "organism": "Agromyces protaetiae", "title": "Agromyces protaetiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004135405.1", "bioproject": "PRJNA224116", "biosample": "SAMN10817494", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2509455", "species_taxid": "2509455", "organism_name": "Agromyces protaetiae", "infraspecific_name": "strain=FW100M-8", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/03", "asm_name": "ASM413540v1", "asm_submitter": "National Institute of Agricultural Sciences", "gbrs_paired_asm": "GCA_004135405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/135/405/GCF_004135405.1_ASM413540v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3683091", "genome_size_ungapped": "3683091", "gc_percent": "70.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004135405.1-RS_2024_04_19", "annotation_date": "2024-04-19", "total_gene_count": "3499", "protein_coding_gene_count": "3312", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-03", "dateModified": "2019-02-03", "datePublished": "2019-02-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Agromyces protaetiae" ], "sample_taxid": [ "2509455" ], "sample_host_organism": [ "Protaetia brevitarsis seulensis larva" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Wanju-gun" ], "sample_host_location_id": [], "data_size": "0.971 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)": "3683091", "Number of Sequences": "1", "Longest Sequences (bp)": "3683091", "N50 (bp)": "3683091", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.5", "Number of CDSs": "3494", "Average Protein Length": "322.0", "Coding Ratio (%)": "91.7", "Number of rRNAs": "9", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Agromyces protaetiae", "strain": "strain=FW100M-8", "accession": "GCA_004135405.1", "taxid": 2509455, "species_taxid": 2509455, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1226, "total_fragments": 1227, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Agromyces agglutinans", "strain": "strain=CFH 90414", "accession": "GCA_009647605.1", "taxid": 2662258, "species_taxid": 2662258, "relation_to_type": "type", "validated": true, "ani": 83.0151, "matched_fragments": 758, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces intestinalis", "strain": "strain=KACC 19306", "accession": "GCA_008365295.1", "taxid": 2592652, "species_taxid": 2592652, "relation_to_type": "type", "validated": true, "ani": 82.4705, "matched_fragments": 797, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces mariniharenae", "strain": "strain=NEAU-184", "accession": "GCA_008122505.1", "taxid": 2604423, "species_taxid": 2604423, "relation_to_type": "type", "validated": true, "ani": 82.3759, "matched_fragments": 768, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces binzhouensis", "strain": "strain=CGMCC 4.7180", "accession": "GCA_004135055.1", "taxid": 1817495, "species_taxid": 1817495, "relation_to_type": "type", "validated": true, "ani": 82.2776, "matched_fragments": 469, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces tardus", "strain": "strain=SJ-23", "accession": "GCA_003710805.1", "taxid": 2583849, "species_taxid": 2583849, "relation_to_type": "type", "validated": true, "ani": 82.2046, "matched_fragments": 693, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces allii", "strain": "strain=JCM 13584", "accession": "GCA_009749385.1", "taxid": 393607, "species_taxid": 393607, "relation_to_type": "type", "validated": true, "ani": 82.1548, "matched_fragments": 775, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces aureus", "strain": "strain=AR33", "accession": "GCA_001660485.1", "taxid": 453304, "species_taxid": 453304, "relation_to_type": "type", "validated": true, "ani": 82.0413, "matched_fragments": 780, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces bracchium", "strain": "strain=JCM 11433", "accession": "GCA_009709675.1", "taxid": 88376, "species_taxid": 88376, "relation_to_type": "type", "validated": true, "ani": 82.01, "matched_fragments": 715, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces aurantiacus", "strain": "strain=DSM 14598", "accession": "GCA_016907355.1", "taxid": 165814, "species_taxid": 165814, "relation_to_type": "type", "validated": true, "ani": 81.987, "matched_fragments": 736, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces mediolanus", "strain": "strain=JCM 3346", "accession": "GCA_014648575.1", "taxid": 41986, "species_taxid": 41986, "relation_to_type": "type", "validated": true, "ani": 81.9186, "matched_fragments": 703, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces cavernae", "strain": "strain=SYSU K20354", "accession": "GCA_021044935.1", "taxid": 2898659, "species_taxid": 2898659, "relation_to_type": "type", "validated": true, "ani": 81.7907, "matched_fragments": 698, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces flavus", "strain": "strain=CPCC 202695", "accession": "GCA_900104685.1", "taxid": 589382, "species_taxid": 589382, "relation_to_type": "type", "validated": true, "ani": 81.7242, "matched_fragments": 676, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces luteolus", "strain": "strain=JCM 11431", "accession": "GCA_009729855.1", "taxid": 88373, "species_taxid": 88373, "relation_to_type": "type", "validated": true, "ani": 81.7029, "matched_fragments": 710, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces marinus", "strain": "strain=DSM 26151", "accession": "GCA_021442325.1", "taxid": 1389020, "species_taxid": 1389020, "relation_to_type": "type", "validated": true, "ani": 81.6893, "matched_fragments": 644, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces flavus", "strain": "strain=CPCC 202695", "accession": "GCA_004366335.2", "taxid": 589382, "species_taxid": 589382, "relation_to_type": "type", "validated": true, "ani": 81.6737, "matched_fragments": 676, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces flavus", "strain": "strain=CCM 7623", "accession": "GCA_014635805.1", "taxid": 589382, "species_taxid": 589382, "relation_to_type": "type", "validated": true, "ani": 81.6466, "matched_fragments": 678, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces archimandritae", "strain": "strain=G127AT", "accession": "GCA_018024495.1", "taxid": 2781962, "species_taxid": 2781962, "relation_to_type": "type", "validated": true, "ani": 80.7977, "matched_fragments": 596, "total_fragments": 1227, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004135405.1", "gtdb_species": "s__Agromyces protaetiae", "ani": 100.0, "matched_fragments": 1227, "total_fragments": 1227, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces", "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": 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