{ "type": "genome", "identifier": "GCF_003667545.1", "organism": "Mycetocola manganoxydans", "title": "Mycetocola manganoxydans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese center for disease control and prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003667545.1", "bioproject": "PRJNA224116", "biosample": "SAMN10234907", "wgs_master": "RCUV00000000.1", "refseq_category": "na", "taxid": "699879", "species_taxid": "699879", "organism_name": "Mycetocola manganoxydans", "infraspecific_name": "strain=CCTCC AB209002", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/21", "asm_name": "ASM366754v1", "asm_submitter": "Chinese center for disease control and prevention", "gbrs_paired_asm": "GCA_003667545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/667/545/GCF_003667545.1_ASM366754v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3060410", "genome_size_ungapped": "3060410", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "32", "contig_count": "32", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003667545.1-RS_2024_09_20", "annotation_date": "2024-09-20", "total_gene_count": "2965", "protein_coding_gene_count": "2888", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-21", "dateModified": "2018-10-21", "datePublished": "2018-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycetocola manganoxydans" ], "sample_taxid": [ "699879" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Xinjiang" ], "sample_host_location_id": [], "data_size": "0.847 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)": "3060410", "Number of Sequences": "32", "Longest Sequences (bp)": "348306", "N50 (bp)": "234603", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.3", "Number of CDSs": "2932", "Average Protein Length": "316.6", "Coding Ratio (%)": "91.0", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycetocola manganoxydans", "strain": "strain=CCTCC AB209002", "accession": "GCA_003667545.1", "taxid": 699879, "species_taxid": 699879, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1006, "total_fragments": 1008, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycetocola manganoxydans", "strain": "strain=KCTC 19753", "accession": "GCA_014651755.1", "taxid": 699879, "species_taxid": 699879, "relation_to_type": "type", "validated": true, "ani": 99.9961, "matched_fragments": 1006, "total_fragments": 1008, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycetocola miduiensis", "strain": "strain=CGMCC 1.11101", "accession": "GCA_900115155.1", "taxid": 995034, "species_taxid": 995034, "relation_to_type": "type", "validated": true, "ani": 81.9421, "matched_fragments": 631, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycetocola zhujimingii", "strain": "strain=449 = CGMCC 1.16372", "accession": "GCA_003065425.1", "taxid": 2079792, "species_taxid": 2079792, "relation_to_type": "type", "validated": true, "ani": 80.5955, "matched_fragments": 533, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycetocola zhadangensis", "strain": "strain=ZD1-4", "accession": "GCA_003668565.1", "taxid": 1164595, "species_taxid": 1164595, "relation_to_type": "type", "validated": true, "ani": 80.1439, "matched_fragments": 493, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycetocola zhadangensis", "strain": "strain=CGMCC 1.12042", "accession": "GCA_014636455.1", "taxid": 1164595, "species_taxid": 1164595, "relation_to_type": "type", "validated": true, "ani": 80.1291, "matched_fragments": 503, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microterricola gilva", "strain": "strain=DSM 18319", "accession": "GCA_004217495.1", "taxid": 393267, "species_taxid": 393267, "relation_to_type": "type", "validated": true, "ani": 78.6981, "matched_fragments": 333, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter californiensis", "strain": "strain=CFBP 8216", "accession": "GCA_003576155.1", "taxid": 1401995, "species_taxid": 1401995, "relation_to_type": "type", "validated": true, "ani": 78.2735, "matched_fragments": 218, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces lapidis", "strain": "strain=JCM 14321", "accession": "GCA_009749405.1", "taxid": 279574, "species_taxid": 279574, "relation_to_type": "type", "validated": true, "ani": 78.1992, "matched_fragments": 345, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter californiensis", "strain": "strain=CFBP 8216", "accession": "GCA_021952865.1", "taxid": 1401995, "species_taxid": 1401995, "relation_to_type": "type", "validated": true, "ani": 78.1393, "matched_fragments": 259, "total_fragments": 1008, "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": 78.1052, "matched_fragments": 273, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces humatus", "strain": "strain=JCM 14319", "accession": "GCA_021228295.1", "taxid": 279573, "species_taxid": 279573, "relation_to_type": "type", "validated": true, "ani": 78.0988, "matched_fragments": 328, "total_fragments": 1008, "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": 78.0976, "matched_fragments": 338, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium allii", "strain": "strain=20TX0166", "accession": "GCA_021271025.1", "taxid": 2878384, "species_taxid": 2878384, "relation_to_type": "type", "validated": true, "ani": 77.679, "matched_fragments": 256, "total_fragments": 1008, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003667545.1", "gtdb_species": "s__Mycetocola_A manganoxydans", "ani": 100.0, "matched_fragments": 1006, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A", "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": "conclusive" }, { "accession": "GCF_900115155.1", "gtdb_species": "s__Mycetocola_A miduiensis", "ani": 81.9461, "matched_fragments": 631, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A", "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_015752285.1", "gtdb_species": "s__Mycetocola_A sp015752285", "ani": 81.6885, "matched_fragments": 650, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A", "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_003065425.1", "gtdb_species": "s__Mycetocola_A zhujimingii", "ani": 80.6072, "matched_fragments": 532, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003668565.1", "gtdb_species": "s__Mycetocola_A zhadangensis", "ani": 80.1372, "matched_fragments": 494, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Mycetocola_A", "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_004801905.1", "gtdb_species": "s__Leifsonia_A flavus", "ani": 78.3821, "matched_fragments": 281, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A", "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_900142065.1", "gtdb_species": "s__Agromyces cerinus", "ani": 78.2228, "matched_fragments": 332, "total_fragments": 1008, "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_003067705.1", "gtdb_species": "s__Planctomonas deserti", "ani": 78.2042, "matched_fragments": 311, "total_fragments": 1008, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Planctomonas", "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_009749405.1", "gtdb_species": "s__Agromyces lapidis", "ani": 78.185, "matched_fragments": 347, "total_fragments": 1008, "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_004216665.1", "gtdb_species": "s__Agromyces ramosus", "ani": 78.1757, "matched_fragments": 328, "total_fragments": 1008, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.456, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.0, "optimum_ph": 7.5, "genome_size": 3375841.75, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycetocola", "manganoxydans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }