{ "type": "genome", "identifier": "GCF_000184285.1", "organism": "Loigolactobacillus coryniformis subsp. torquens DSM 20004 = KCTC 3535", "title": "Loigolactobacillus coryniformis subsp. torquens DSM 20004 = KCTC 3535", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Korea Research Institute of Bioscience and Biotechnology (KRIBB)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000184285.1", "bioproject": "PRJNA224116", "biosample": "SAMN02470831", "wgs_master": "AEOS00000000.1", "refseq_category": "na", "taxid": "1423822", "species_taxid": "1610", "organism_name": "Loigolactobacillus coryniformis subsp. torquens DSM 20004 = KCTC 3535", "infraspecific_name": "strain=KCTC 3535", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2010/12/17", "asm_name": "ASM18428v1", "asm_submitter": "Korea Research Institute of Bioscience and Biotechnology (KRIBB)", "gbrs_paired_asm": "GCA_000184285.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/184/285/GCF_000184285.1_ASM18428v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2815780", "genome_size_ungapped": "2815780", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "433", "contig_count": "433", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000184285.1-RS_2024_11_18", "annotation_date": "2024-11-18", "total_gene_count": "2931", "protein_coding_gene_count": "2663", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2010-12-17", "dateModified": "2010-12-17", "datePublished": "2010-12-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Loigolactobacillus coryniformis subsp. torquens DSM 20004 = KCTC 3535" ], "sample_taxid": [ "1423822" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.807 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2811629", "Number of Sequences": "402", "Longest Sequences (bp)": "61848", "N50 (bp)": "14726", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.9", "Number of CDSs": "2693", "Average Protein Length": "279.7", "Coding Ratio (%)": "80.4", "Number of rRNAs": "2", "Number of tRNAs": "51", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Loigolactobacillus coryniformis subsp. torquens", "strain": "strain=KCTC 3535", "accession": "GCA_000184285.2", "taxid": 115542, "species_taxid": 1610, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 743, "total_fragments": 759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Loigolactobacillus coryniformis subsp. torquens", "strain": "strain=DSM 20004", "accession": "GCA_001435425.1", "taxid": 115542, "species_taxid": 1610, "relation_to_type": "type", "validated": true, "ani": 99.8793, "matched_fragments": 699, "total_fragments": 759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Loigolactobacillus coryniformis subsp. torquens", "strain": "strain=DSM 20004", "accession": "GCA_002706705.1", "taxid": 115542, "species_taxid": 1610, "relation_to_type": "type", "validated": true, "ani": 99.8785, "matched_fragments": 754, "total_fragments": 759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Loigolactobacillus coryniformis subsp. coryniformis", "strain": "strain=DSM 20001", "accession": "GCA_001433765.1", "taxid": 115541, "species_taxid": 1610, "relation_to_type": "type", "validated": true, "ani": 97.6994, "matched_fragments": 598, "total_fragments": 759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Loigolactobacillus coryniformis subsp. coryniformis", "strain": "strain=KCTC 3167", "accession": "GCA_000166795.1", "taxid": 115541, "species_taxid": 1610, "relation_to_type": "type", "validated": true, "ani": 97.5929, "matched_fragments": 674, "total_fragments": 759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Loigolactobacillus coryniformis subsp. coryniformis", "strain": "strain=DSM 20001", "accession": "GCA_002706425.1", "taxid": 115541, "species_taxid": 1610, "relation_to_type": "type", "validated": true, "ani": 97.5074, "matched_fragments": 635, "total_fragments": 759, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Loigolactobacillus jiayinensis", "strain": "strain=257-1", "accession": "GCA_003946445.1", "taxid": 2486016, "species_taxid": 2486016, "relation_to_type": "type", "validated": true, "ani": 81.0471, "matched_fragments": 452, "total_fragments": 759, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Loigolactobacillus zhaoyuanensis", "strain": "strain=187-3", "accession": "GCA_003946385.1", "taxid": 2486017, "species_taxid": 2486017, "relation_to_type": "type", "validated": true, "ani": 80.8622, "matched_fragments": 401, "total_fragments": 759, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_002706425.1", "gtdb_species": "s__Loigolactobacillus coryniformis", "ani": 97.5074, "matched_fragments": 635, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.81", "num_clustered_genomes": 10, "status": "conclusive" }, { "accession": "GCF_005405165.1", "gtdb_species": "s__Loigolactobacillus binensis", "ani": 81.5936, "matched_fragments": 396, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "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_003946445.1", "gtdb_species": "s__Loigolactobacillus jiayinensis", "ani": 81.0617, "matched_fragments": 452, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "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_003946385.1", "gtdb_species": "s__Loigolactobacillus zhaoyuanensis", "ani": 80.8759, "matched_fragments": 400, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "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_003946275.1", "gtdb_species": "s__Loigolactobacillus backii", "ani": 80.2572, "matched_fragments": 109, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_003950295.1", "gtdb_species": "s__Loigolactobacillus iwatensis", "ani": 78.7181, "matched_fragments": 124, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "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_001434575.1", "gtdb_species": "s__Loigolactobacillus bifermentans", "ani": 78.2598, "matched_fragments": 99, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001436505.1", "gtdb_species": "s__Loigolactobacillus rennini", "ani": 77.8672, "matched_fragments": 140, "total_fragments": 759, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "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": [ "Loigolactobacillus", "coryniformis", "subsp.", "torquens", "DSM", "20004", "=", "KCTC", "3535" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }