{ "type": "genome", "identifier": "GCF_014527425.1", "organism": "Listeria innocua", "title": "Listeria innocua", "description": "na", "data type": "Genome sequencing and assembly", "organization": "PulseNet USA", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014527425.1", "bioproject": "PRJNA224116", "biosample": "SAMN13941777", "wgs_master": "JABXLC000000000.1", "refseq_category": "na", "taxid": "1642", "species_taxid": "1642", "organism_name": "Listeria innocua", "infraspecific_name": "strain=F4078", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/11", "asm_name": "ASM1452742v1", "asm_submitter": "PulseNet USA", "gbrs_paired_asm": "GCA_014527425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/527/425/GCF_014527425.1_ASM1452742v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2857635", "genome_size_ungapped": "2857635", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "12", "contig_count": "12", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014527425.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "2863", "protein_coding_gene_count": "2778", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-11", "dateModified": "2020-09-11", "datePublished": "2020-09-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Listeria innocua" ], "sample_taxid": [ "1642" ], "sample_host_organism": [ "cow" ], "sample_host_organism_id": [], "sample_host_disease": [ "missing" ], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.806 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)": "2857635", "Number of Sequences": "12", "Longest Sequences (bp)": "1407369", "N50 (bp)": "540209", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.4", "Number of CDSs": "2814", "Average Protein Length": "304.9", "Coding Ratio (%)": "90.1", "Number of rRNAs": "2", "Number of tRNAs": "53", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Listeria innocua", "strain": "strain=F4078", "accession": "GCA_014527425.1", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 948, "total_fragments": 948, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria innocua", "strain": "strain=F4078", "accession": "GCA_024721565.1", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "type", "validated": true, "ani": 99.9952, "matched_fragments": 947, "total_fragments": 948, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria innocua", "strain": "strain=H0996", "accession": "GCA_017363655.2", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "claderef", "validated": true, "ani": 98.8237, "matched_fragments": 887, "total_fragments": 948, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria innocua", "strain": "strain=2010L-2059", "accession": "GCA_017363615.2", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "claderef", "validated": true, "ani": 96.5377, "matched_fragments": 856, "total_fragments": 948, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria farberi", "strain": "strain=FSL L7-0091", "accession": "GCA_014229245.1", "taxid": 2713500, "species_taxid": 2713500, "relation_to_type": "type", "validated": true, "ani": 92.4292, "matched_fragments": 831, "total_fragments": 948, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria monocytogenes", "strain": "strain=G4599", "accession": "GCA_001466295.1", "taxid": 1639, "species_taxid": 1639, "relation_to_type": "claderef", "validated": true, "ani": 89.3872, "matched_fragments": 829, "total_fragments": 948, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria monocytogenes", "strain": "strain=J0099", "accession": "GCA_013625995.1", "taxid": 1639, "species_taxid": 1639, "relation_to_type": "claderef", "validated": true, "ani": 89.3419, "matched_fragments": 833, "total_fragments": 948, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria swaminathanii", "strain": "strain=FSL L7-0020", "accession": "GCA_014229645.1", "taxid": 2713501, "species_taxid": 2713501, "relation_to_type": "type", "validated": true, "ani": 88.4731, "matched_fragments": 778, "total_fragments": 948, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_015276835.1", "gtdb_species": "s__Listeria innocua", "ani": 98.7901, "matched_fragments": 888, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "96.24", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 107, "status": "conclusive" }, { "accession": "GCF_014229245.1", "gtdb_species": "s__Listeria farberi", "ani": 92.4292, "matched_fragments": 831, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000307025.1", "gtdb_species": "s__Listeria monocytogenes_B", "ani": 89.325, "matched_fragments": 838, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "95.21", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.90", "num_clustered_genomes": 1699, "status": "-" }, { "accession": "GCF_900187225.1", "gtdb_species": "s__Listeria monocytogenes", "ani": 89.0901, "matched_fragments": 812, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "95.98", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.89", "num_clustered_genomes": 1977, "status": "-" }, { "accession": "GCF_013282665.1", "gtdb_species": "s__Listeria monocytogenes_C", "ani": 88.6845, "matched_fragments": 813, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.79", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 176, "status": "-" }, { "accession": "GCF_014229645.1", "gtdb_species": "s__Listeria sp014229645", "ani": 88.4731, "matched_fragments": 778, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "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_014224155.1", "gtdb_species": "s__Listeria cossartiae", "ani": 88.3876, "matched_fragments": 801, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.01", "min_intra_species_ani": "97.44", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_014229095.1", "gtdb_species": "s__Listeria cayugensis", "ani": 88.1605, "matched_fragments": 803, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.39", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000060285.1", "gtdb_species": "s__Listeria welshimeri", "ani": 87.5454, "matched_fragments": 775, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.96", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 49, "status": "-" }, { "accession": "GCF_014322765.1", "gtdb_species": "s__Listeria immobilis", "ani": 83.6415, "matched_fragments": 678, "total_fragments": 948, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.373, "cell_length": 0.255, "doubling_h": -0.328, "growth_tmp": 32.5, "optimum_tmp": 34.375, "optimum_ph": 7.125, "genome_size": 2965990.0, "gc_content": 37.006, "coding_genes": 3060.5, "rRNA16S_genes": 6.0, "tRNA_genes": 66.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Listeria", "innocua" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }