{ "type": "genome", "identifier": "GCF_000237995.1", "organism": "Pediococcus claussenii ATCC BAA-344", "title": "Pediococcus claussenii ATCC BAA-344", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Saskatchewan", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000237995.1", "bioproject": "PRJNA224116", "biosample": "SAMN02604240", "wgs_master": "na", "refseq_category": "na", "taxid": "701521", "species_taxid": "187452", "organism_name": "Pediococcus claussenii ATCC BAA-344", "infraspecific_name": "strain=ATCC BAA-344", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/03/15", "asm_name": "ASM23799v2", "asm_submitter": "University of Saskatchewan", "gbrs_paired_asm": "GCA_000237995.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/237/995/GCF_000237995.1_ASM23799v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1978793", "genome_size_ungapped": "1978793", "gc_percent": "37.000000", "replicon_count": "9", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-16", "total_gene_count": "1956", "protein_coding_gene_count": "1853", "non_coding_gene_count": "73", "pubmed_id": "22328764" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-03-15", "dateModified": "2012-03-15", "datePublished": "2012-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Pediococcus claussenii ATCC BAA-344" ], "sample_taxid": [ "701521" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.557 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)": "1978793", "Number of Sequences": "9", "Longest Sequences (bp)": "1829111", "N50 (bp)": "1829111", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.0", "Number of CDSs": "1919", "Average Protein Length": "298.7", "Coding Ratio (%)": "86.9", "Number of rRNAs": "12", "Number of tRNAs": "57", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pediococcus claussenii", "strain": "strain=ATCC BAA-344", "accession": "GCA_000237995.2", "taxid": 187452, "species_taxid": 187452, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 655, "total_fragments": 655, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pediococcus claussenii", "strain": "strain=DSM 14800", "accession": "GCA_001436905.1", "taxid": 187452, "species_taxid": 187452, "relation_to_type": "type", "validated": true, "ani": 99.9211, "matched_fragments": 610, "total_fragments": 655, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Liquorilactobacillus nagelii", "strain": "strain=DSM 13675", "accession": "GCA_019444005.1", "taxid": 82688, "species_taxid": 82688, "relation_to_type": "type", "validated": true, "ani": 79.5886, "matched_fragments": 57, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus parvulus", "strain": "strain=JCM 5889", "accession": "GCA_014651215.1", "taxid": 54062, "species_taxid": 54062, "relation_to_type": "type", "validated": true, "ani": 78.8398, "matched_fragments": 81, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus parvulus", "strain": "strain=NBRC 100673", "accession": "GCA_007990205.1", "taxid": 54062, "species_taxid": 54062, "relation_to_type": "type", "validated": true, "ani": 78.6857, "matched_fragments": 78, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus argentinicus", "strain": "strain=DSM 23026", "accession": "GCA_001437605.1", "taxid": 480391, "species_taxid": 480391, "relation_to_type": "type", "validated": true, "ani": 78.6668, "matched_fragments": 127, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus ethanolidurans", "strain": "strain=DSM 22301", "accession": "GCA_001437405.1", "taxid": 319653, "species_taxid": 319653, "relation_to_type": "type", "validated": true, "ani": 78.3296, "matched_fragments": 80, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus argentinicus", "strain": "strain=CCUG 54535", "accession": "GCA_012396535.1", "taxid": 480391, "species_taxid": 480391, "relation_to_type": "type", "validated": true, "ani": 78.2521, "matched_fragments": 122, "total_fragments": 655, "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": 78.1779, "matched_fragments": 50, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus ethanolidurans", "strain": "strain=CGMCC 1.3889", "accession": "GCA_900111205.1", "taxid": 319653, "species_taxid": 319653, "relation_to_type": "type", "validated": true, "ani": 78.0064, "matched_fragments": 79, "total_fragments": 655, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000237995.1", "gtdb_species": "s__Pediococcus claussenii", "ani": 100.0, "matched_fragments": 655, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.79", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_002970935.1", "gtdb_species": "s__Lactiplantibacillus sp002970935", "ani": 83.94, "matched_fragments": 55, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus", "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_002970915.1", "gtdb_species": "s__Lactiplantibacillus sp002970915", "ani": 81.4124, "matched_fragments": 51, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus", "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_001437285.1", "gtdb_species": "s__Pediococcus pentosaceus", "ani": 78.9044, "matched_fragments": 113, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 75, "status": "-" }, { "accession": "GCF_007990205.1", "gtdb_species": "s__Pediococcus parvulus", "ani": 78.6857, "matched_fragments": 78, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001437605.1", "gtdb_species": "s__Pediococcus argentinicus", "ani": 78.6668, "matched_fragments": 127, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001437405.1", "gtdb_species": "s__Pediococcus ethanolidurans", "ani": 78.3296, "matched_fragments": 80, "total_fragments": 655, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "97.25", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001434225.1", "gtdb_species": "s__Liquorilactobacillus nagelii", "ani": 78.2133, "matched_fragments": 51, "total_fragments": 655, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.16, "cell_length": -0.158, "doubling_h": null, "growth_tmp": 31.0, "optimum_tmp": 36.833, "optimum_ph": 6.316, "genome_size": 1960894.222, "gc_content": 38.217, "coding_genes": 1846.4, "rRNA16S_genes": 4.0, "tRNA_genes": 57.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pediococcus", "claussenii", "ATCC", "BAA-344" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }