{ "type": "genome", "identifier": "GCF_001437255.1", "organism": "Pediococcus damnosus", "title": "Pediococcus damnosus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shanghai Majorbio", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001437255.1", "bioproject": "PRJNA224116", "biosample": "SAMN02797815", "wgs_master": "JQBD00000000.1", "refseq_category": "na", "taxid": "51663", "species_taxid": "51663", "organism_name": "Pediococcus damnosus", "infraspecific_name": "strain=DSM 20331", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/06", "asm_name": "ASM143725v1", "asm_submitter": "Shanghai Majorbio", "gbrs_paired_asm": "GCA_001437255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/437/255/GCF_001437255.1_ASM143725v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2191735", "genome_size_ungapped": "2191735", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "201", "contig_count": "201", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001437255.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "2165", "protein_coding_gene_count": "2046", "non_coding_gene_count": "54", "pubmed_id": "26415554" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-11-06", "dateModified": "2015-11-06", "datePublished": "2015-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pediococcus damnosus" ], "sample_taxid": [ "51663" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.625 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)": "2191735", "Number of Sequences": "201", "Longest Sequences (bp)": "70015", "N50 (bp)": "20859", "Gap Ratio (%)": "0.000639", "GCcontent (%)": "38.2", "Number of CDSs": "2075", "Average Protein Length": "294.5", "Coding Ratio (%)": "83.7", "Number of rRNAs": "1", "Number of tRNAs": "48", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pediococcus damnosus", "strain": "strain=DSM 20331", "accession": "GCA_001437255.1", "taxid": 51663, "species_taxid": 51663, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 646, "total_fragments": 648, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pediococcus inopinatus", "strain": "strain=DSM 20285", "accession": "GCA_002982135.1", "taxid": 114090, "species_taxid": 114090, "relation_to_type": "type", "validated": true, "ani": 82.7933, "matched_fragments": 456, "total_fragments": 648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus inopinatus", "strain": "strain=DSM 20285", "accession": "GCA_001438725.1", "taxid": 114090, "species_taxid": 114090, "relation_to_type": "type", "validated": true, "ani": 82.6289, "matched_fragments": 440, "total_fragments": 648, "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": 79.9352, "matched_fragments": 284, "total_fragments": 648, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pediococcus parvulus", "strain": "strain=NBRC 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"GCA_001311505.1", "taxid": 1193095, "species_taxid": 1193095, "relation_to_type": "type", "validated": true, "ani": 79.3284, "matched_fragments": 69, "total_fragments": 648, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001437255.1", "gtdb_species": "s__Pediococcus damnosus", "ani": 100.0, "matched_fragments": 646, "total_fragments": 648, "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": "conclusive" }, { "accession": "GCF_002982135.1", "gtdb_species": "s__Pediococcus inopinatus", "ani": 82.7933, "matched_fragments": 456, "total_fragments": 648, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "98.95", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_007990205.1", "gtdb_species": "s__Pediococcus parvulus", "ani": 79.85, "matched_fragments": 277, "total_fragments": 648, "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": 79.8448, "matched_fragments": 310, "total_fragments": 648, "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_003946385.1", "gtdb_species": "s__Loigolactobacillus zhaoyuanensis", "ani": 79.6133, "matched_fragments": 50, "total_fragments": 648, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Loigolactobacillus", "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_001438655.1", "gtdb_species": "s__Pediococcus cellicola", "ani": 79.5914, "matched_fragments": 242, "total_fragments": 648, "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_001437605.1", "gtdb_species": "s__Pediococcus argentinicus", "ani": 78.6717, "matched_fragments": 75, "total_fragments": 648, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.16, "cell_length": -0.158, "doubling_h": null, "growth_tmp": 26.0, "optimum_tmp": 36.833, "optimum_ph": 6.316, "genome_size": 2295171.667, "gc_content": 38.37, "coding_genes": 2124.0, "rRNA16S_genes": 4.0, "tRNA_genes": 62.0, "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", "damnosus" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }