{ "type": "genome", "identifier": "GCF_004364555.1", "organism": "Amnibacterium kyonggiense", "title": "Amnibacterium kyonggiense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004364555.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621476", "wgs_master": "SOAM00000000.1", "refseq_category": "reference genome", "taxid": "595671", "species_taxid": "595671", "organism_name": "Amnibacterium kyonggiense", "infraspecific_name": "strain=DSM 24782", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436455v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004364555.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/364/555/GCF_004364555.1_ASM436455v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3709865", "genome_size_ungapped": "3709865", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004364555.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "3701", "protein_coding_gene_count": "3623", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Amnibacterium kyonggiense" ], "sample_taxid": [ "595671" ], "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": "0.966 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)": "3709865", "Number of Sequences": "6", "Longest Sequences (bp)": "1649177", "N50 (bp)": "997725", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "73.1", "Number of CDSs": "3674", "Average Protein Length": "309.1", "Coding Ratio (%)": "91.8", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Amnibacterium kyonggiense", "strain": "strain=DSM 24782", "accession": "GCA_004364555.1", "taxid": 595671, "species_taxid": 595671, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1233, "total_fragments": 1233, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Amnibacterium setariae", "strain": "strain=DD4a", "accession": "GCA_003581425.1", "taxid": 2306585, "species_taxid": 2306585, "relation_to_type": "type", "validated": true, "ani": 85.3681, "matched_fragments": 887, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=CFBP 2404", "accession": "GCA_003693415.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.537, "matched_fragments": 431, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. insidiosus", "strain": "strain=ATCC 10253", "accession": "GCA_003076355.1", "taxid": 33014, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.5286, "matched_fragments": 437, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rathayibacter festucae", "strain": "strain=DSM 15932", "accession": "GCA_004011135.1", "taxid": 110937, "species_taxid": 110937, "relation_to_type": "type", "validated": true, "ani": 78.4378, "matched_fragments": 513, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis", "strain": "strain=LMG7333", "accession": "GCA_021216655.1", "taxid": 28447, "species_taxid": 28447, "relation_to_type": "suspected-type", "validated": true, "ani": 78.4261, "matched_fragments": 431, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_002240635.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.4248, "matched_fragments": 463, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter michiganensis subsp. tessellarius", "strain": "strain=ATCC 33566", "accession": "GCA_021922985.1", "taxid": 31965, "species_taxid": 28447, "relation_to_type": "type", "validated": true, "ani": 78.419, "matched_fragments": 457, "total_fragments": 1233, "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": 78.3407, "matched_fragments": 468, "total_fragments": 1233, "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": 78.282, "matched_fragments": 472, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rathayibacter caricis", "strain": "strain=DSM 15933", "accession": "GCA_003044275.1", "taxid": 110936, "species_taxid": 110936, "relation_to_type": "type", "validated": true, "ani": 78.2271, "matched_fragments": 470, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces ramosus", "strain": "strain=DSM 43045", "accession": "GCA_004216665.1", "taxid": 33879, "species_taxid": 33879, "relation_to_type": "type", "validated": true, "ani": 78.2234, "matched_fragments": 436, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Protaetiibacter intestinalis", "strain": "strain=2DFWR-13", "accession": "GCA_003627075.1", "taxid": 2419774, "species_taxid": 2419774, "relation_to_type": "type", "validated": true, "ani": 78.2015, "matched_fragments": 429, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium citreum", "strain": "strain=LMG8786T", "accession": "GCA_024997915.1", "taxid": 2036, "species_taxid": 2036, "relation_to_type": "type", "validated": true, "ani": 78.152, "matched_fragments": 435, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium citreum", "strain": "strain=JCM 1345", "accession": "GCA_014646735.1", "taxid": 2036, "species_taxid": 2036, "relation_to_type": "type", "validated": true, "ani": 78.0787, "matched_fragments": 445, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium citreum", "strain": "strain=DSM 20528", "accession": "GCA_006715175.1", "taxid": 2036, "species_taxid": 2036, "relation_to_type": "type", "validated": true, "ani": 78.0234, "matched_fragments": 449, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gryllotalpicola protaetiae", "strain": "strain=2DFW10M-5", "accession": "GCA_003627055.1", "taxid": 2419771, "species_taxid": 2419771, "relation_to_type": "type", "validated": true, "ani": 78.0171, "matched_fragments": 409, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus sediminis", "strain": "strain=NS18", "accession": "GCA_007923295.1", "taxid": 2599924, "species_taxid": 2599924, "relation_to_type": "type", "validated": true, "ani": 78.0135, "matched_fragments": 418, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrococcus carbonis", "strain": "strain=DSM 22965", "accession": "GCA_900104705.1", "taxid": 684552, "species_taxid": 684552, "relation_to_type": "type", "validated": true, "ani": 77.8701, "matched_fragments": 412, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium thalassium", "strain": "strain=DSM 12511", "accession": "GCA_014208045.1", "taxid": 362649, "species_taxid": 362649, "relation_to_type": "type", "validated": true, "ani": 77.6745, "matched_fragments": 384, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium kyungheense", "strain": "strain=DSM 105492", "accession": "GCA_006783905.1", "taxid": 1263636, "species_taxid": 1263636, "relation_to_type": "type", "validated": true, "ani": 77.5018, "matched_fragments": 384, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium ulmi", "strain": "strain=JCM 14282", "accession": "GCA_013004565.1", "taxid": 179095, "species_taxid": 179095, "relation_to_type": "type", "validated": true, "ani": 77.4921, "matched_fragments": 360, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium ulmi", "strain": "strain=CECT 5976", "accession": "GCA_011759705.1", "taxid": 179095, "species_taxid": 179095, "relation_to_type": "type", "validated": true, "ani": 77.4052, "matched_fragments": 374, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004364555.1", "gtdb_species": "s__Amnibacterium kyonggiense", "ani": 100.0, "matched_fragments": 1233, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium", "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_003581425.1", "gtdb_species": "s__Amnibacterium setariae", "ani": 85.4149, "matched_fragments": 883, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Amnibacterium", "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_003384945.1", "gtdb_species": "s__Clavibacter sp003384945", "ani": 78.5119, "matched_fragments": 455, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter", "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_004011135.1", "gtdb_species": "s__Rathayibacter festucae", "ani": 78.4747, "matched_fragments": 509, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.98", "min_intra_species_ani": "96.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_009866655.1", "gtdb_species": "s__Rathayibacter sp009866655", "ani": 78.4253, "matched_fragments": 503, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.89", "min_intra_species_ani": "98.89", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_006517535.1", "gtdb_species": "s__Schumannella sp006517535", "ani": 78.3493, "matched_fragments": 441, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella", "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_008122505.1", "gtdb_species": "s__Agromyces sp008122505", "ani": 78.3237, "matched_fragments": 470, "total_fragments": 1233, "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": "-" }, { "accession": "GCF_001705035.1", "gtdb_species": "s__Curtobacterium sp001705035", "ani": 78.3168, "matched_fragments": 428, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "98.72", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013205055.1", "gtdb_species": "s__Rathayibacter sp013205055", "ani": 78.2996, "matched_fragments": 511, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter", "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_003627075.1", "gtdb_species": "s__Protaetiibacter intestinalis", "ani": 78.2187, "matched_fragments": 427, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", 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"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_004216665.1", "gtdb_species": "s__Agromyces ramosus", "ani": 78.159, "matched_fragments": 443, "total_fragments": 1233, "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": "-" }, { "accession": "GCF_001806325.1", "gtdb_species": "s__Curtobacterium sp001806325", "ani": 78.1545, "matched_fragments": 426, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004959775.1", "gtdb_species": "s__Agromyces sp004959775", "ani": 78.0967, "matched_fragments": 442, "total_fragments": 1233, "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": "-" }, { "accession": "GCF_009765225.1", "gtdb_species": "s__Leifsonia sp009765225", "ani": 78.0768, "matched_fragments": 398, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", 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