{ "type": "genome", "identifier": "GCA_022484185.1", "organism": "Lacticaseibacillus paracasei", "title": "Lacticaseibacillus paracasei", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_022484185.1", "bioproject": "PRJNA768539", "biosample": "SAMN22412520", "wgs_master": "JAKVLV000000000.1", "refseq_category": "na", "taxid": "1597", "species_taxid": "1597", "organism_name": "Lacticaseibacillus paracasei", "infraspecific_name": "", "isolate": "UW_TS_LACCAS1_3", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/03/05", "asm_name": "ASM2248418v1", "submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/022/484/185/GCA_022484185.1_ASM2248418v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-03-05", "dateModified": "2022-03-05", "datePublished": "2022-03-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Lacticaseibacillus paracasei" ], "sample_taxid": [ "1597" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Madison, WI", "Freezer" ], "sample_host_location_id": [], "data_size": "0.851 MB", "sample_ph_range": { "min": 55.0, "max": 55.0 }, "sample_temperature_range": { "min": 35.0, "max": 80.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3003404", "Number of Sequences": "3", "Longest Sequences (bp)": "2626612", "N50 (bp)": "2626612", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "46.6", "Number of CDSs": "2864", "Average Protein Length": "295.1", "Coding Ratio (%)": "84.4", "Number of rRNAs": "15", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lacticaseibacillus paracasei subsp. paracasei", "strain": "strain=DSM 5622", "accession": "GCA_001436385.1", "taxid": 47714, "species_taxid": 1597, "relation_to_type": "type", "validated": true, "ani": 98.3513, "matched_fragments": 814, "total_fragments": 999, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lacticaseibacillus paracasei subsp. paracasei", "strain": "strain=ATCC 25302", "accession": "GCA_004354655.1", "taxid": 47714, "species_taxid": 1597, "relation_to_type": "type", "validated": true, "ani": 98.2741, "matched_fragments": 840, "total_fragments": 999, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lacticaseibacillus paracasei subsp. paracasei", "strain": "strain=NBRC 15889", "accession": "GCA_007989125.1", "taxid": 47714, "species_taxid": 1597, "relation_to_type": "type", "validated": true, "ani": 98.2546, "matched_fragments": 818, "total_fragments": 999, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lacticaseibacillus paracasei subsp. paracasei", "strain": "strain=ATCC 25302", "accession": "GCA_000159495.1", "taxid": 47714, "species_taxid": 1597, "relation_to_type": "type", "validated": true, "ani": 98.1698, "matched_fragments": 865, "total_fragments": 999, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lacticaseibacillus paracasei subsp. paracasei", "strain": "strain=JCM 8130", "accession": "GCA_000829035.1", "taxid": 47714, "species_taxid": 1597, "relation_to_type": "type", "validated": true, "ani": 98.1374, "matched_fragments": 867, "total_fragments": 999, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lacticaseibacillus casei", "strain": "strain=ATCC 393", "accession": "GCA_000829055.1", "taxid": 1582, "species_taxid": 1582, "relation_to_type": "suspected-type", "validated": true, "ani": 80.9868, "matched_fragments": 428, "total_fragments": 999, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000829035.1", "gtdb_species": "s__Lacticaseibacillus paracasei", "ani": 98.1609, "matched_fragments": 867, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "97.86", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.73", "num_clustered_genomes": 252, "status": "conclusive" }, { "accession": "GCF_000829055.1", "gtdb_species": "s__Lacticaseibacillus casei", "ani": 80.9686, "matched_fragments": 431, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.80", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_000260435.1", "gtdb_species": "s__Lacticaseibacillus zeae", "ani": 80.605, "matched_fragments": 434, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_900636965.1", "gtdb_species": "s__Lacticaseibacillus rhamnosus", "ani": 80.5081, "matched_fragments": 438, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "96.73", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 237, "status": "-" }, { "accession": "GCF_004123795.1", "gtdb_species": "s__Lacticaseibacillus chiayiensis", "ani": 80.0595, "matched_fragments": 410, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "98.62", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003946165.1", "gtdb_species": "s__Lacticaseibacillus baoqingensis", "ani": 78.3375, "matched_fragments": 73, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "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_001311785.1", "gtdb_species": "s__Lacticaseibacillus saniviri", "ani": 78.0752, "matched_fragments": 75, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.88", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001436115.1", "gtdb_species": "s__Lacticaseibacillus brantae", "ani": 76.9506, "matched_fragments": 70, "total_fragments": 999, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus", "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lacticaseibacillus", "s__Lacticaseibacillus paracasei" ], "_genome_taxon": [ "Lacticaseibacillus", "paracasei", "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lacticaseibacillus", "s__Lacticaseibacillus paracasei", "Bacteria", "Bacillota", "Bacilli", "Lactobacillales", "Lactobacillaceae", "Lacticaseibacillus", "Lacticaseibacillus", "paracasei" ], "_meo": [ { "id": "MEO_0000119", "label": "bioreactor" } ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }