{ "type": "genome", "identifier": "GCF_029916425.1", "organism": "Liquorilactobacillus sicerae", "title": "Liquorilactobacillus sicerae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of the Basque Country", "publication": [ {} ], "properties": { "assembly_accession": "GCF_029916425.1", "bioproject": "PRJNA224116", "biosample": "SAMN19104997", "wgs_master": "JAHAVQ000000000.1", "refseq_category": "reference genome", "taxid": "1416943", "species_taxid": "1416943", "organism_name": "Liquorilactobacillus sicerae", "infraspecific_name": "strain=CUPV261", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/05/01", "asm_name": "ASM2991642v1", "asm_submitter": "University of the Basque Country", "gbrs_paired_asm": "GCA_029916425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/029/916/425/GCF_029916425.1_ASM2991642v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2426367", "genome_size_ungapped": "2426367", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "404", "contig_count": "404", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_029916425.1-RS_2024_05_13", "annotation_date": "2024-05-13", "total_gene_count": "2611", "protein_coding_gene_count": "2330", "non_coding_gene_count": "75", "pubmed_id": "37086527" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-05-01", "dateModified": "2023-05-01", "datePublished": "2023-05-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Liquorilactobacillus sicerae" ], "sample_taxid": [ "1416943" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain" ], "sample_host_location_id": [], "data_size": "0.692 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.63, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2426367", "Number of Sequences": "404", "Longest Sequences (bp)": "232311", "N50 (bp)": "129263", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.5", "Number of CDSs": "2187", "Average Protein Length": "297.8", "Coding Ratio (%)": "80.5", "Number of rRNAs": "5", "Number of tRNAs": "57", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Liquorilactobacillus vini", "strain": "strain=DSM 20605", "accession": "GCA_000255495.2", "taxid": 238015, "species_taxid": 238015, "relation_to_type": "type", "validated": true, "ani": 87.2395, "matched_fragments": 524, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus vini", "strain": "strain=DSM 20605", "accession": "GCA_001435395.1", "taxid": 238015, "species_taxid": 238015, "relation_to_type": "type", "validated": true, "ani": 87.1565, "matched_fragments": 521, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus nagelii", "strain": "strain=DSM 13675", "accession": "GCA_019444005.1", "taxid": 82688, "species_taxid": 82688, "relation_to_type": "type", "validated": true, "ani": 78.5896, "matched_fragments": 209, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus nagelii", "strain": "strain=DSM 13675", "accession": "GCA_001434225.1", "taxid": 82688, "species_taxid": 82688, "relation_to_type": "type", "validated": true, "ani": 78.3963, "matched_fragments": 196, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus ghanensis", "strain": "strain=DSM 18630", "accession": "GCA_001435235.1", "taxid": 399370, "species_taxid": 399370, "relation_to_type": "type", "validated": true, "ani": 77.7991, "matched_fragments": 209, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus mali", "strain": "strain=KCTC 3596", "accession": "GCA_000260415.1", "taxid": 1618, "species_taxid": 1618, "relation_to_type": "type", "validated": true, "ani": 77.4487, "matched_fragments": 93, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus mali", "strain": "strain=DSM 20444", "accession": "GCA_001436535.1", "taxid": 1618, "species_taxid": 1618, "relation_to_type": "type", "validated": true, "ani": 77.2625, "matched_fragments": 84, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus uvarum", "strain": "strain=DSM 19971", "accession": "GCA_001434935.1", "taxid": 303240, "species_taxid": 303240, "relation_to_type": "type", "validated": true, "ani": 77.1952, "matched_fragments": 109, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus oeni", "strain": "strain=DSM 19972", "accession": "GCA_001436275.1", "taxid": 303241, "species_taxid": 303241, "relation_to_type": "type", "validated": true, "ani": 77.1404, "matched_fragments": 85, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ligilactobacillus acidipiscis", "strain": "strain=DSM 15836", "accession": "GCA_001435755.1", "taxid": 89059, "species_taxid": 89059, "relation_to_type": "type", "validated": true, "ani": 76.9535, "matched_fragments": 50, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Liquorilactobacillus cacaonum", "strain": "strain=DSM 21116", "accession": "GCA_001436735.1", "taxid": 483012, "species_taxid": 483012, "relation_to_type": "type", "validated": true, "ani": 76.8677, "matched_fragments": 83, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ligilactobacillus apodemi", "strain": "strain=DSM 16634", "accession": "GCA_001434405.1", "taxid": 307126, "species_taxid": 307126, "relation_to_type": "type", "validated": true, "ani": 76.7112, "matched_fragments": 53, "total_fragments": 730, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.63, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000255495.1", "gtdb_species": "s__Liquorilactobacillus vini", "ani": 87.2641, "matched_fragments": 524, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001434225.1", "gtdb_species": "s__Liquorilactobacillus nagelii", "ani": 78.3963, "matched_fragments": 196, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.67", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001437155.1", "gtdb_species": "s__Liquorilactobacillus mali_A", "ani": 77.9408, "matched_fragments": 94, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "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_001435235.1", "gtdb_species": "s__Liquorilactobacillus ghanensis", "ani": 77.7991, "matched_fragments": 209, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "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_000260415.1", "gtdb_species": "s__Liquorilactobacillus mali", "ani": 77.4768, "matched_fragments": 93, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001434935.1", "gtdb_species": "s__Liquorilactobacillus uvarum", "ani": 77.1952, "matched_fragments": 109, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "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_001436275.1", "gtdb_species": "s__Liquorilactobacillus oeni", "ani": 77.1404, "matched_fragments": 85, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "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_001435755.1", "gtdb_species": "s__Ligilactobacillus acidipiscis", "ani": 76.9535, "matched_fragments": 50, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.76", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001436735.1", "gtdb_species": "s__Liquorilactobacillus cacaonum", "ani": 76.8677, "matched_fragments": 83, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "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_001434405.1", "gtdb_species": "s__Ligilactobacillus apodemi", "ani": 76.7082, "matched_fragments": 52, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000612445.1", "gtdb_species": "s__Liquorilactobacillus sucicola", "ani": 76.5925, "matched_fragments": 85, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus", "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": 2, "status": "-" }, { "accession": "GCF_000423245.1", "gtdb_species": "s__Ligilactobacillus ceti", "ani": 76.5416, "matched_fragments": 51, "total_fragments": 730, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "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": [ "Liquorilactobacillus", "sicerae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }