{ "type": "genome", "identifier": "GCF_003946005.1", "organism": "Companilactobacillus allii", "title": "Companilactobacillus allii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northeast Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003946005.1", "bioproject": "PRJNA224116", "biosample": "SAMN10357369", "wgs_master": "RHNV00000000.1", "refseq_category": "na", "taxid": "1847728", "species_taxid": "1847728", "organism_name": "Companilactobacillus allii", "infraspecific_name": "strain=JCM 31938", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/14", "asm_name": "ASM394600v1", "asm_submitter": "Northeast Agricultural University", "gbrs_paired_asm": "GCA_003946005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/946/005/GCF_003946005.1_ASM394600v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2520831", "genome_size_ungapped": "2520831", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003946005.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "2553", "protein_coding_gene_count": "2470", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-14", "dateModified": "2018-12-14", "datePublished": "2018-12-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Companilactobacillus allii" ], "sample_taxid": [ "1847728" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.708 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)": "2520831", "Number of Sequences": "17", "Longest Sequences (bp)": "558692", "N50 (bp)": "314734", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.3", "Number of CDSs": "2519", "Average Protein Length": "296.8", "Coding Ratio (%)": "89.0", "Number of rRNAs": "2", "Number of tRNAs": "54", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Companilactobacillus allii", "strain": "strain=JCM 31938", "accession": "GCA_003946005.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 832, "total_fragments": 833, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus allii", "strain": "strain=WiKim39", "accession": "GCA_001971585.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 99.9963, "matched_fragments": 829, "total_fragments": 833, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus allii", "strain": "strain=WiKim39", "accession": "GCA_023923085.1", "taxid": 1847728, "species_taxid": 1847728, "relation_to_type": "type", "validated": true, "ani": 99.992, "matched_fragments": 827, "total_fragments": 833, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Companilactobacillus hulinensis", "strain": "strain=8-1(1)", "accession": "GCA_003946555.1", "taxid": 2486007, "species_taxid": 2486007, "relation_to_type": "type", "validated": true, "ani": 83.4529, "matched_fragments": 534, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus nodensis", "strain": "strain=DSM 19682", "accession": "GCA_001435555.1", "taxid": 460870, "species_taxid": 460870, "relation_to_type": "type", "validated": true, "ani": 82.0456, "matched_fragments": 428, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus jidongensis", "strain": "strain=204-8", "accession": "GCA_003946575.1", "taxid": 2486006, "species_taxid": 2486006, "relation_to_type": "type", "validated": true, "ani": 81.7545, "matched_fragments": 461, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus insicii", "strain": "strain=DSM 29801", "accession": "GCA_003946015.1", "taxid": 1732567, "species_taxid": 1732567, "relation_to_type": "type", "validated": true, "ani": 81.4478, "matched_fragments": 410, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus baiquanensis", "strain": "strain=184-8", "accession": "GCA_003946605.1", "taxid": 2486005, "species_taxid": 2486005, "relation_to_type": "type", "validated": true, "ani": 79.9273, "matched_fragments": 278, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus kimchii", "strain": "strain=DSM 13961", "accession": "GCA_009764365.1", "taxid": 2801452, "species_taxid": 2801452, "relation_to_type": "type", "validated": true, "ani": 79.5972, "matched_fragments": 268, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus mishanensis", "strain": "strain=256-3", "accession": "GCA_003946505.1", "taxid": 2486008, "species_taxid": 2486008, "relation_to_type": "type", "validated": true, "ani": 79.4554, "matched_fragments": 203, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus huachuanensis", "strain": "strain=395-6.2", "accession": "GCA_005404815.1", "taxid": 2559914, "species_taxid": 2559914, "relation_to_type": "type", "validated": true, "ani": 79.2146, "matched_fragments": 263, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus paralimentarius", "strain": "strain=DSM 13238", "accession": "GCA_009764345.1", "taxid": 83526, "species_taxid": 83526, "relation_to_type": "type", "validated": true, "ani": 79.2017, "matched_fragments": 266, "total_fragments": 833, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001971585.1", "gtdb_species": "s__Companilactobacillus allii", "ani": 99.9963, "matched_fragments": 829, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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": "conclusive" }, { "accession": "GCF_003946555.1", "gtdb_species": "s__Companilactobacillus hulinensis", "ani": 83.4697, "matched_fragments": 533, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_000615905.1", "gtdb_species": "s__Companilactobacillus nodensis", "ani": 81.8756, "matched_fragments": 429, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003946575.1", "gtdb_species": "s__Companilactobacillus jidongensis", "ani": 81.7545, "matched_fragments": 461, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_003946015.1", "gtdb_species": "s__Companilactobacillus insicii", "ani": 81.4485, "matched_fragments": 409, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_003946605.1", "gtdb_species": "s__Companilactobacillus baiquanensis", "ani": 79.9482, "matched_fragments": 278, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_001434665.1", "gtdb_species": "s__Companilactobacillus tucceti", "ani": 79.5507, "matched_fragments": 286, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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_009600985.1", "gtdb_species": "s__Companilactobacillus halodurans", "ani": 79.4394, "matched_fragments": 238, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.75", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009764355.1", "gtdb_species": "s__Companilactobacillus paralimentarius_A", "ani": 79.2899, "matched_fragments": 289, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.92", "min_intra_species_ani": "99.92", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_005404815.1", "gtdb_species": "s__Companilactobacillus huachuanensis", "ani": 79.2324, "matched_fragments": 262, "total_fragments": 833, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "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": [ "Companilactobacillus", "allii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }