{ "type": "genome", "identifier": "GCF_002563955.1", "organism": "Paramicrobacterium agarici", "title": "Paramicrobacterium agarici", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002563955.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488572", "wgs_master": "PDJE00000000.1", "refseq_category": "na", "taxid": "630514", "species_taxid": "630514", "organism_name": "Paramicrobacterium agarici", "infraspecific_name": "strain=DSM 21798", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/10/17", "asm_name": "ASM256395v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_002563955.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/563/955/GCF_002563955.1_ASM256395v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3233920", "genome_size_ungapped": "3233920", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002563955.1-RS_2024_06_23", "annotation_date": "2024-06-23", "total_gene_count": "3163", "protein_coding_gene_count": "3086", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-10-17", "dateModified": "2017-10-17", "datePublished": "2017-10-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Paramicrobacterium agarici" ], "sample_taxid": [ "630514" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.891 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)": "3233920", "Number of Sequences": "1", "Longest Sequences (bp)": "3233920", "N50 (bp)": "3233920", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.5", "Number of CDSs": "3120", "Average Protein Length": "319.2", "Coding Ratio (%)": "92.4", "Number of rRNAs": "6", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbacterium agarici", "strain": "strain=DSM 21798", "accession": "GCA_002563955.1", "taxid": 630514, "species_taxid": 630514, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1075, "total_fragments": 1077, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Microbacterium lindanitolerans", "strain": "strain=DSM 22422", "accession": "GCA_006788875.1", "taxid": 550448, "species_taxid": 550448, "relation_to_type": "type", "validated": true, "ani": 97.5201, "matched_fragments": 999, "total_fragments": 1077, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Microbacterium fandaimingii", "strain": "strain=HY82", "accession": "GCA_011751745.2", "taxid": 2708079, "species_taxid": 2708079, "relation_to_type": "type", "validated": true, "ani": 81.2678, "matched_fragments": 714, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium chengjingii", "strain": "strain=HY60", "accession": "GCA_011751765.2", "taxid": 2769067, "species_taxid": 2769067, "relation_to_type": "type", "validated": true, "ani": 80.7538, "matched_fragments": 678, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium humi", "strain": "strain=DSM 21799", "accession": "GCA_900105715.1", "taxid": 640635, "species_taxid": 640635, "relation_to_type": "type", "validated": true, "ani": 80.1447, "matched_fragments": 554, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces agglutinans", "strain": "strain=CFH 90414", "accession": "GCA_009647605.1", "taxid": 2662258, "species_taxid": 2662258, "relation_to_type": "type", "validated": true, "ani": 77.9889, "matched_fragments": 286, "total_fragments": 1077, "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": 77.9415, "matched_fragments": 225, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium commune", "strain": "strain=Re1", "accession": "GCA_014836945.1", "taxid": 2762219, "species_taxid": 2762219, "relation_to_type": "type", "validated": true, "ani": 77.8456, "matched_fragments": 224, "total_fragments": 1077, "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": 77.7761, "matched_fragments": 288, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium esteraromaticum", "strain": "strain=DSM 8609", "accession": "GCA_016907315.1", "taxid": 57043, "species_taxid": 57043, "relation_to_type": "suspected-type", "validated": true, "ani": 77.6262, "matched_fragments": 229, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium pullorum", "strain": "strain=Sa4CUA7", "accession": "GCA_014836535.1", "taxid": 2762236, "species_taxid": 2762236, "relation_to_type": "type", "validated": true, "ani": 77.516, "matched_fragments": 210, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium yannicii", "strain": "strain=DSM 23203", "accession": "GCA_024055635.1", "taxid": 671622, "species_taxid": 671622, "relation_to_type": "type", "validated": true, "ani": 77.4417, "matched_fragments": 232, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sulfonylureivorans", "strain": "strain=LAM7116", "accession": "GCA_003999995.1", "taxid": 2486854, "species_taxid": 2486854, "relation_to_type": "type", "validated": true, "ani": 77.4073, "matched_fragments": 235, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium flaccumfaciens", "strain": "strain=LMG3645", "accession": "GCA_024997845.1", "taxid": 2035, "species_taxid": 2035, "relation_to_type": "suspected-type", "validated": true, "ani": 77.2105, "matched_fragments": 195, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia merdavium", "strain": "strain=Sa2CUA9", "accession": "GCA_014836755.1", "taxid": 2762227, "species_taxid": 2762227, "relation_to_type": "type", "validated": true, "ani": 76.3627, "matched_fragments": 144, "total_fragments": 1077, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002563955.1", "gtdb_species": "s__Microbacterium_A agarici", "ani": 100.0, "matched_fragments": 1075, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.53", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_011751745.2", "gtdb_species": "s__Microbacterium_A fandaimingii", "ani": 81.2521, "matched_fragments": 716, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "98.82", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011751765.2", "gtdb_species": "s__Microbacterium_A chengjingii", "ani": 80.7538, "matched_fragments": 678, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900105715.1", "gtdb_species": "s__Microbacterium_A humi", "ani": 80.1545, "matched_fragments": 553, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium_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_900115155.1", "gtdb_species": "s__Mycetocola_A miduiensis", "ani": 78.009, "matched_fragments": 222, "total_fragments": 1077, "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_003627075.1", "gtdb_species": "s__Protaetiibacter intestinalis", "ani": 77.9415, "matched_fragments": 225, "total_fragments": 1077, "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", "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_001428255.1", "gtdb_species": "s__Agromyces sp001428255", "ani": 77.936, "matched_fragments": 266, "total_fragments": 1077, "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_004959775.1", "gtdb_species": "s__Agromyces sp004959775", "ani": 77.9109, "matched_fragments": 277, "total_fragments": 1077, "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_004078635.1", "gtdb_species": "s__Labedella phragmitis", "ani": 77.9103, "matched_fragments": 288, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella", "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_014483895.1", "gtdb_species": "s__Protaetiibacter sp014483895", "ani": 77.8183, "matched_fragments": 244, "total_fragments": 1077, "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", "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": 77.7124, "matched_fragments": 215, "total_fragments": 1077, "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_003990045.1", "gtdb_species": "s__Labedella endophytica", "ani": 77.6783, "matched_fragments": 267, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Labedella", "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_001513675.1", "gtdb_species": "s__Microbacterium sp001513675", "ani": 77.6329, "matched_fragments": 231, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_017831975.1", "gtdb_species": "s__Microbacterium terrae", "ani": 77.5949, "matched_fragments": 240, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_010686705.1", "gtdb_species": "s__Diaminobutyricibacter tongyongensis", "ani": 77.5874, "matched_fragments": 226, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricibacter", "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_017355965.1", "gtdb_species": "s__JAFIQW01 sp017355965", "ani": 77.5314, "matched_fragments": 260, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAFIQW01", "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_002325245.1", "gtdb_species": "s__Pseudolysinimonas sp002325245", "ani": 77.4744, "matched_fragments": 188, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudolysinimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.78", "min_intra_species_ani": "99.17", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_002362255.1", "gtdb_species": "s__Microbacterium sp002362255", "ani": 77.425, "matched_fragments": 227, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_003999995.1", "gtdb_species": "s__Microbacterium sp003999995", "ani": 77.4199, "matched_fragments": 234, "total_fragments": 1077, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Paramicrobacterium", "agarici" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }