{ "type": "genome", "identifier": "GCF_003399685.1", "organism": "Subtercola boreus", "title": "Subtercola boreus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea Polar Research Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003399685.1", "bioproject": "PRJNA224116", "biosample": "SAMN06610376", "wgs_master": "NBWZ00000000.1", "refseq_category": "na", "taxid": "120213", "species_taxid": "120213", "organism_name": "Subtercola boreus", "infraspecific_name": "strain=K300", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/16", "asm_name": "ASM339968v1", "asm_submitter": "Korea Polar Research Institute", "gbrs_paired_asm": "GCA_003399685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/399/685/GCF_003399685.1_ASM339968v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4212750", "genome_size_ungapped": "4212750", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003399685.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "3946", "protein_coding_gene_count": "3858", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-16", "dateModified": "2018-08-16", "datePublished": "2018-08-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Subtercola boreus" ], "sample_taxid": [ "120213" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Incheon" ], "sample_host_location_id": [], "data_size": "1.144 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 17.0, "max": 17.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4212750", "Number of Sequences": "2", "Longest Sequences (bp)": "4047544", "N50 (bp)": "4047544", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.0", "Number of CDSs": "3937", "Average Protein Length": "328.7", "Coding Ratio (%)": "92.2", "Number of rRNAs": "6", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Subtercola boreus", "strain": "strain=K300", "accession": "GCA_003399685.1", "taxid": 120213, "species_taxid": 120213, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1402, "total_fragments": 1404, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Subtercola boreus", "strain": "strain=DSM 13056", "accession": "GCA_006716115.1", "taxid": 120213, "species_taxid": 120213, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9994, "matched_fragments": 1402, "total_fragments": 1404, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Subtercola vilae", "strain": "strain=DB165", "accession": "GCA_004923255.1", "taxid": 2056433, "species_taxid": 2056433, "relation_to_type": "type", "validated": true, "ani": 80.9854, "matched_fragments": 621, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Subtercola frigoramans", "strain": "strain=DSM 13057", "accession": "GCA_016907385.1", "taxid": 120298, "species_taxid": 120298, "relation_to_type": "type", "validated": true, "ani": 80.6013, "matched_fragments": 566, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Subtercola lobariae", "strain": "strain=9583b", "accession": "GCA_016881145.1", "taxid": 1588641, "species_taxid": 1588641, "relation_to_type": "type", "validated": true, "ani": 80.1151, "matched_fragments": 575, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Subtercola lobariae", "strain": "strain=CGMCC 1.12976", "accession": "GCA_014640255.1", "taxid": 1588641, "species_taxid": 1588641, "relation_to_type": "type", "validated": true, "ani": 80.0623, "matched_fragments": 575, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbiconiux flava", "strain": "strain=DSM 26474", "accession": "GCA_013409865.1", "taxid": 881268, "species_taxid": 881268, "relation_to_type": "type", "validated": true, "ani": 79.9408, "matched_fragments": 561, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbiconiux solani", "strain": "strain=NBRC 106740", "accession": "GCA_001571005.1", "taxid": 661329, "species_taxid": 661329, "relation_to_type": "type", "validated": true, "ani": 79.7912, "matched_fragments": 514, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbiconiux ginsengi", "strain": "strain=CGMCC 4.3491", "accession": "GCA_900107435.1", "taxid": 381665, "species_taxid": 381665, "relation_to_type": "type", "validated": true, "ani": 79.3784, "matched_fragments": 522, "total_fragments": 1404, "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": 78.5161, "matched_fragments": 422, "total_fragments": 1404, "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": 78.4206, "matched_fragments": 383, "total_fragments": 1404, "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": 78.4104, "matched_fragments": 404, "total_fragments": 1404, "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": 78.3905, "matched_fragments": 412, "total_fragments": 1404, "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": 78.2787, "matched_fragments": 356, "total_fragments": 1404, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006716115.1", "gtdb_species": "s__Subtercola boreus", "ani": 99.9994, "matched_fragments": 1401, "total_fragments": 1404, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola", "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_003399635.1", "gtdb_species": "s__Subtercola boreus_B", "ani": 86.9341, "matched_fragments": 941, "total_fragments": 1404, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola", "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_003399625.1", "gtdb_species": "s__Subtercola boreus_C", "ani": 86.6993, "matched_fragments": 963, "total_fragments": 1404, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola", "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_002931235.1", "gtdb_species": "s__Subtercola sp002931235", "ani": 84.5804, "matched_fragments": 787, "total_fragments": 1404, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola", "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_003399645.1", "gtdb_species": "s__Subtercola boreus_A", "ani": 83.3778, "matched_fragments": 835, "total_fragments": 1404, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola", "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": 3, "status": "-" }, { "accession": "GCF_018889995.1", "gtdb_species": "s__Subtercola sp018889995", "ani": 80.4161, "matched_fragments": 565, "total_fragments": 1404, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Subtercola", "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": -0.699, "cell_length": -0.222, "doubling_h": null, "growth_tmp": 24.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": null, "motility": null, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Subtercola", "boreus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }