{ "type": "genome", "identifier": "GCF_016127775.1", "organism": "Pediococcus pentosaceus", "title": "Pediococcus pentosaceus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016127775.1", "bioproject": "PRJNA224116", "biosample": "SAMN16357178", "wgs_master": "na", "refseq_category": "na", "taxid": "1255", "species_taxid": "1255", "organism_name": "Pediococcus pentosaceus", "infraspecific_name": "strain=FDAARGOS_1009", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/20", "asm_name": "ASM1612777v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_016127775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/127/775/GCF_016127775.1_ASM1612777v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1751923", "genome_size_ungapped": "1751923", "gc_percent": "37.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-18", "total_gene_count": "1731", "protein_coding_gene_count": "1627", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-20", "dateModified": "2020-12-20", "datePublished": "2020-12-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Pediococcus pentosaceus" ], "sample_taxid": [ "1255" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Braunschweig" ], "sample_host_location_id": [], "data_size": "0.495 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)": "1751923", "Number of Sequences": "2", "Longest Sequences (bp)": "1717965", "N50 (bp)": "1717965", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.4", "Number of CDSs": "1690", "Average Protein Length": "302.6", "Coding Ratio (%)": "87.6", "Number of rRNAs": "15", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pediococcus pentosaceus", "strain": "strain=FDAARGOS_1009", "accession": "GCA_016127775.1", "taxid": 1255, "species_taxid": 1255, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 583, "total_fragments": 583, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pediococcus pentosaceus", "strain": "strain=ATCC 33316", "accession": "GCA_004354495.1", "taxid": 1255, "species_taxid": 1255, "relation_to_type": "type", "validated": true, "ani": 99.9833, "matched_fragments": 570, "total_fragments": 583, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pediococcus pentosaceus", "strain": "strain=DSM 20336", "accession": "GCA_001437285.1", "taxid": 1255, "species_taxid": 1255, "relation_to_type": "type", "validated": true, "ani": 99.9725, "matched_fragments": 557, "total_fragments": 583, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pediococcus acidilactici", "strain": "strain=CCUG 32235", "accession": "GCA_012396515.1", "taxid": 1254, "species_taxid": 1254, "relation_to_type": "neotype", "validated": true, "ani": 79.6104, "matched_fragments": 193, "total_fragments": 583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Companilactobacillus pabuli", "strain": "strain=NFFJ11", "accession": "GCA_014058425.1", "taxid": 2714036, "species_taxid": 2714036, "relation_to_type": "type", "validated": true, "ani": 79.5415, "matched_fragments": 53, "total_fragments": 583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus acidilactici", "strain": "strain=DSM 20284", "accession": "GCA_000146325.1", "taxid": 1254, "species_taxid": 1254, "relation_to_type": "neotype", "validated": true, "ani": 79.4778, "matched_fragments": 192, "total_fragments": 583, "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": 79.0915, "matched_fragments": 142, "total_fragments": 583, "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": 78.6622, "matched_fragments": 138, "total_fragments": 583, "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": 78.5234, "matched_fragments": 71, "total_fragments": 583, "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": 78.3508, "matched_fragments": 66, "total_fragments": 583, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus kosonis", "strain": "strain=NBRC111893", "accession": "GCA_003864335.1", "taxid": 2810561, "species_taxid": 2810561, "relation_to_type": "type", "validated": true, "ani": 77.5826, "matched_fragments": 54, "total_fragments": 583, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001437285.1", "gtdb_species": "s__Pediococcus pentosaceus", "ani": 99.9725, "matched_fragments": 557, "total_fragments": 583, "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": "conclusive" }, { "accession": "GCF_001437075.1", "gtdb_species": "s__Pediococcus stilesii", "ani": 80.0431, "matched_fragments": 247, "total_fragments": 583, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "97.68", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009809575.1", "gtdb_species": "s__Pediococcus acidilactici_A", "ani": 79.893, "matched_fragments": 181, "total_fragments": 583, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "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_000146325.1", "gtdb_species": "s__Pediococcus acidilactici", "ani": 79.4778, "matched_fragments": 192, "total_fragments": 583, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.64", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.81", "num_clustered_genomes": 172, "status": "-" }, { "accession": "GCF_000260415.1", "gtdb_species": "s__Liquorilactobacillus mali", "ani": 79.2495, "matched_fragments": 50, "total_fragments": 583, "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_014058425.1", "gtdb_species": "s__Companilactobacillus pabuli", "ani": 79.115, "matched_fragments": 52, "total_fragments": 583, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001437605.1", "gtdb_species": "s__Pediococcus argentinicus", "ani": 79.0978, "matched_fragments": 143, "total_fragments": 583, "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_007990205.1", "gtdb_species": "s__Pediococcus parvulus", "ani": 78.3508, "matched_fragments": 66, "total_fragments": 583, "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_001437405.1", "gtdb_species": "s__Pediococcus ethanolidurans", "ani": 78.1533, "matched_fragments": 75, "total_fragments": 583, "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_001438655.1", "gtdb_species": "s__Pediococcus cellicola", "ani": 78.0766, "matched_fragments": 66, "total_fragments": 583, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001437255.1", "gtdb_species": "s__Pediococcus damnosus", "ani": 77.9419, "matched_fragments": 65, "total_fragments": 583, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.57", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 12, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.16, "cell_length": -0.158, "doubling_h": null, "growth_tmp": 31.0, "optimum_tmp": 32.333, "optimum_ph": 6.316, "genome_size": 1831777.0, "gc_content": 37.246, "coding_genes": 1694.0, "rRNA16S_genes": 5.0, "tRNA_genes": 54.625, "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", "pentosaceus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }