{ "type": "genome", "identifier": "GCF_018327645.1", "organism": "Lactobacillus corticis", "title": "Lactobacillus corticis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Central Region Agricultural Research Center, NARO", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018327645.1", "bioproject": "PRJNA224116", "biosample": "SAMD00236747", "wgs_master": "BMAY00000000.1", "refseq_category": "reference genome", "taxid": "2201249", "species_taxid": "2201249", "organism_name": "Lactobacillus corticis", "infraspecific_name": "strain=B40", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/03/26", "asm_name": "ASM1832764v1", "asm_submitter": "Central Region Agricultural Research Center, NARO", "gbrs_paired_asm": "GCA_018327645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/327/645/GCF_018327645.1_ASM1832764v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1805525", "genome_size_ungapped": "1805525", "gc_percent": "42.000000", "replicon_count": "0", "scaffold_count": "115", "contig_count": "115", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018327645.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "1801", "protein_coding_gene_count": "1664", "non_coding_gene_count": "98", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-03-26", "dateModified": "2021-03-26", "datePublished": "2021-03-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Lactobacillus corticis" ], "sample_taxid": [ "2201249" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "0.511 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)": "1805525", "Number of Sequences": "115", "Longest Sequences (bp)": "299761", "N50 (bp)": "170905", "Gap Ratio (%)": "0.000443", "GCcontent (%)": "42.2", "Number of CDSs": "1666", "Average Protein Length": "319.8", "Coding Ratio (%)": "88.5", "Number of rRNAs": "4", "Number of tRNAs": "64", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lactobacillus corticis", "strain": "strain=B40", "accession": "GCA_018327645.1", "taxid": 2201249, "species_taxid": 2201249, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 580, "total_fragments": 581, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lactobacillus acidophilus", "strain": "strain=ATCC 4356", "accession": "GCA_000786395.1", "taxid": 1579, "species_taxid": 1579, "relation_to_type": "type", "validated": true, "ani": 79.0959, "matched_fragments": 110, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus kitasatonis", "strain": "strain=JCM 1039", "accession": "GCA_000615285.1", "taxid": 237446, "species_taxid": 237446, "relation_to_type": "type", "validated": true, "ani": 79.0918, "matched_fragments": 133, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus kitasatonis", "strain": "strain=DSM 16761", "accession": "GCA_001434435.1", "taxid": 237446, "species_taxid": 237446, "relation_to_type": "type", "validated": true, "ani": 79.0519, "matched_fragments": 133, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus acidophilus", "strain": "strain=CIP 76.13", "accession": "GCA_000469705.1", "taxid": 1579, "species_taxid": 1579, "relation_to_type": "type", "validated": true, "ani": 79.0052, "matched_fragments": 112, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus acidophilus", "strain": "strain=DSM 20079", "accession": "GCA_003047065.1", "taxid": 1579, "species_taxid": 1579, "relation_to_type": "type", "validated": true, "ani": 79.0005, "matched_fragments": 116, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylovorus", "strain": "strain=DSM 20531", "accession": "GCA_002706375.1", "taxid": 1604, "species_taxid": 1604, "relation_to_type": "type", "validated": true, "ani": 78.997, "matched_fragments": 130, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylovorus", "strain": "strain=DSM 20531", "accession": "GCA_001433985.1", "taxid": 1604, "species_taxid": 1604, "relation_to_type": "type", "validated": true, "ani": 78.9558, "matched_fragments": 129, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus acidophilus", "strain": "strain=DSM 20079", "accession": "GCA_001433895.1", "taxid": 1579, "species_taxid": 1579, "relation_to_type": "type", "validated": true, "ani": 78.8517, "matched_fragments": 109, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylolyticus", "strain": "strain=DSM 11664", "accession": "GCA_004354545.1", "taxid": 83683, "species_taxid": 83683, "relation_to_type": "type", "validated": true, "ani": 78.8113, "matched_fragments": 117, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus equicursoris", "strain": "strain=JCM 14600", "accession": "GCA_001311765.1", "taxid": 420645, "species_taxid": 420645, "relation_to_type": "type", "validated": true, "ani": 78.7667, "matched_fragments": 79, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus xujianguonis", "strain": "strain=HT111-2", "accession": "GCA_004009905.1", "taxid": 2495899, "species_taxid": 2495899, "relation_to_type": "type", "validated": true, "ani": 78.7602, "matched_fragments": 129, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylolyticus", "strain": "strain=DSM 11664", "accession": "GCA_000178475.1", "taxid": 83683, "species_taxid": 83683, "relation_to_type": "type", "validated": true, "ani": 78.6604, "matched_fragments": 114, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus amylolyticus", "strain": "strain=DSM 11664", "accession": "GCA_001435665.1", "taxid": 83683, "species_taxid": 83683, "relation_to_type": "type", "validated": true, "ani": 78.6398, "matched_fragments": 114, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus mulieris", "strain": "strain=c10Ua161M", "accession": "GCA_007095465.1", "taxid": 2508708, "species_taxid": 2508708, "relation_to_type": "type", "validated": true, "ani": 78.4373, "matched_fragments": 91, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus equicursoris", "strain": "strain=type strain:CIP 110162", "accession": "GCA_000312645.1", "taxid": 420645, "species_taxid": 420645, "relation_to_type": "type", "validated": true, "ani": 78.3803, "matched_fragments": 81, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus equicursoris", "strain": "strain=DSM 19284", "accession": "GCA_001434815.1", "taxid": 420645, "species_taxid": 420645, "relation_to_type": "type", "validated": true, "ani": 78.3208, "matched_fragments": 80, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus rodentium", "strain": "strain=DSM 24759", "accession": "GCA_024622425.1", "taxid": 947835, "species_taxid": 947835, "relation_to_type": "type", "validated": true, "ani": 78.165, "matched_fragments": 66, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus apis", "strain": "strain=LMG 26964", "accession": "GCA_002837055.1", "taxid": 303541, "species_taxid": 303541, "relation_to_type": "type", "validated": true, "ani": 78.0111, "matched_fragments": 68, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lactobacillus apis", "strain": "strain=CCM 8403", "accession": "GCA_014635365.1", "taxid": 303541, "species_taxid": 303541, "relation_to_type": "type", "validated": true, "ani": 77.9675, "matched_fragments": 72, "total_fragments": 581, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018327645.1", "gtdb_species": "s__Lactobacillus corticis", "ani": 100.0, "matched_fragments": 580, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "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": "conclusive" }, { "accession": "GCF_001591845.1", "gtdb_species": "s__Lactobacillus acidophilus", "ani": 79.1223, "matched_fragments": 109, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.94", "num_clustered_genomes": 59, "status": "-" }, { "accession": "GCF_000615285.1", "gtdb_species": "s__Lactobacillus kitasatonis", "ani": 79.0781, "matched_fragments": 135, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "97.76", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000615445.1", "gtdb_species": "s__Lactobacillus hamsteri", "ani": 79.0771, "matched_fragments": 106, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001434975.1", "gtdb_species": "s__Lactobacillus gallinarum", "ani": 79.0662, "matched_fragments": 120, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_002706375.1", "gtdb_species": "s__Lactobacillus amylovorus", "ani": 78.9898, "matched_fragments": 130, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.43", "min_intra_species_ani": "96.81", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.78", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_004009905.1", "gtdb_species": "s__Lactobacillus xujianguonis", "ani": 78.7602, "matched_fragments": 129, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.83", "min_intra_species_ani": "99.82", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018987235.1", "gtdb_species": "s__Lactobacillus crispatus", "ani": 78.7104, "matched_fragments": 132, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.75", "min_intra_species_ani": "96.25", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.70", "num_clustered_genomes": 161, "status": "-" }, { "accession": "GCF_000178475.1", "gtdb_species": "s__Lactobacillus amylolyticus", "ani": 78.648, "matched_fragments": 115, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.87", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_007095465.1", "gtdb_species": "s__Lactobacillus mulieris", "ani": 78.4373, "matched_fragments": 91, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "96.91", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_001436305.1", "gtdb_species": "s__Lactobacillus ultunensis", "ani": 78.4314, "matched_fragments": 122, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_007570935.1", "gtdb_species": "s__Lactobacillus sp007570935", "ani": 78.3254, "matched_fragments": 106, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "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_001434815.1", "gtdb_species": "s__Lactobacillus equicursoris", "ani": 78.2849, "matched_fragments": 80, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "97.67", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_009695985.1", "gtdb_species": "s__Lactobacillus porci", "ani": 78.1942, "matched_fragments": 69, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "97.20", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002418055.1", "gtdb_species": "s__Lactobacillus sp002418055", "ani": 78.0472, "matched_fragments": 77, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.82", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001436775.1", "gtdb_species": "s__Lactobacillus acetotolerans", "ani": 78.0195, "matched_fragments": 83, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.02", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_002837055.1", "gtdb_species": "s__Lactobacillus apis", "ani": 78.0155, "matched_fragments": 68, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.63", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_003423665.1", "gtdb_species": "s__Lactobacillus rodentium", "ani": 77.9876, "matched_fragments": 67, "total_fragments": 581, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus", "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": -0.148, "cell_length": 0.354, "doubling_h": -0.086, "growth_tmp": 32.808, "optimum_tmp": 31.646, "optimum_ph": 6.027, "genome_size": 2295637.558, "gc_content": 40.393, "coding_genes": 2119.007, "rRNA16S_genes": 5.074, "tRNA_genes": 63.614, "gram_stain": 1.0, "sporulation": 0.009, "motility": 0.08, "range_salinity": 0.0, "facultative_respiration": 0.155, "anaerobic_respiration": 0.175, "aerobic_respiration": 0.668, "mesophilic_range_tmp": 0.977, "thermophilic_range_tmp": 0.022, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.983, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.016, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Lactobacillus", "corticis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }