{ "type": "genome", "identifier": "GCF_013820765.1", "organism": "Listeria rustica", "title": "Listeria rustica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Cornell University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013820765.1", "bioproject": "PRJNA224116", "biosample": "SAMN14840816", "wgs_master": "JABJVM000000000.1", "refseq_category": "reference genome", "taxid": "2713503", "species_taxid": "2713503", "organism_name": "Listeria rustica", "infraspecific_name": "strain=FSL W9-0585", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/28", "asm_name": "ASM1382076v1", "asm_submitter": "Cornell University", "gbrs_paired_asm": "GCA_013820765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/820/765/GCF_013820765.1_ASM1382076v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3488648", "genome_size_ungapped": "3488648", "gc_percent": "42.000000", "replicon_count": "0", "scaffold_count": "65", "contig_count": "65", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013820765.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "3349", "protein_coding_gene_count": "3248", "non_coding_gene_count": "80", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-28", "dateModified": "2020-07-28", "datePublished": "2020-07-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Listeria rustica" ], "sample_taxid": [ "2713503" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: New York" ], "sample_host_location_id": [], "data_size": "0.994 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)": "3488648", "Number of Sequences": "65", "Longest Sequences (bp)": "394430", "N50 (bp)": "171825", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.2", "Number of CDSs": "3294", "Average Protein Length": "307.8", "Coding Ratio (%)": "87.2", "Number of rRNAs": "2", "Number of tRNAs": "63", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Listeria rustica", "strain": "strain=FSL W9-0585", "accession": "GCA_013820765.1", "taxid": 2713503, "species_taxid": 2713503, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1135, "total_fragments": 1139, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria portnoyi", "strain": "strain=FSL L7-1582", "accession": "GCA_014322795.1", "taxid": 2713504, "species_taxid": 2713504, "relation_to_type": "type", "validated": true, "ani": 94.4593, "matched_fragments": 874, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria newyorkensis", "strain": "strain=FSL M6-0635", "accession": "GCA_000766145.1", "taxid": 1497681, "species_taxid": 1497681, "relation_to_type": "type", "validated": true, "ani": 89.6955, "matched_fragments": 882, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria newyorkensis", "strain": "strain=NCTC13937", "accession": "GCA_900461625.1", "taxid": 1497681, "species_taxid": 1497681, "relation_to_type": "type", "validated": true, "ani": 89.5999, "matched_fragments": 889, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria cornellensis", "strain": "strain=FSL F6-0969", "accession": "GCA_000525855.1", "taxid": 1494961, "species_taxid": 1494961, "relation_to_type": "type", "validated": true, "ani": 89.4276, "matched_fragments": 846, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria rocourtiae", "strain": "strain=FSL F6-920", "accession": "GCA_000525975.1", "taxid": 647910, "species_taxid": 647910, "relation_to_type": "type", "validated": true, "ani": 84.0047, "matched_fragments": 738, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria monocytogenes", "strain": "strain=2014L-6393", "accession": "GCA_013626145.1", "taxid": 1639, "species_taxid": 1639, "relation_to_type": "claderef", "validated": true, "ani": 77.7233, "matched_fragments": 153, "total_fragments": 1139, "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": 77.7083, "matched_fragments": 155, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria innocua", "strain": "strain=H0996", "accession": "GCA_017363655.2", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "claderef", "validated": true, "ani": 77.6902, "matched_fragments": 163, "total_fragments": 1139, "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": 77.6392, "matched_fragments": 181, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria monocytogenes", "strain": "strain=2014L-6256", "accession": "GCA_013625895.1", "taxid": 1639, "species_taxid": 1639, "relation_to_type": "claderef", "validated": true, "ani": 77.5886, "matched_fragments": 177, "total_fragments": 1139, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013820765.1", "gtdb_species": "s__Listeria_A rustica", "ani": 100.0, "matched_fragments": 1135, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "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": "conclusive" }, { "accession": "GCF_014322795.1", "gtdb_species": "s__Listeria_A portnoyi", "ani": 94.4687, "matched_fragments": 873, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "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_000766145.1", "gtdb_species": "s__Listeria_A newyorkensis", "ani": 89.683, "matched_fragments": 883, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "95.80", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_000525855.1", "gtdb_species": "s__Listeria_A cornellensis", "ani": 89.4049, "matched_fragments": 848, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "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_003534205.1", "gtdb_species": "s__Listeria_A weihenstephanensis", "ani": 86.3338, "matched_fragments": 801, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000525835.1", "gtdb_species": "s__Listeria_A grandensis", "ani": 84.6186, "matched_fragments": 759, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.47", "min_intra_species_ani": "97.36", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000525975.1", "gtdb_species": "s__Listeria_A rocourtiae", "ani": 84.0146, "matched_fragments": 737, "total_fragments": 1139, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.373, "cell_length": 0.255, "doubling_h": -0.172, "growth_tmp": 33.572, "optimum_tmp": 33.742, "optimum_ph": 7.125, "genome_size": 3044220.429, "gc_content": 38.83, "coding_genes": 2870.001, "rRNA16S_genes": 5.861, "tRNA_genes": 66.686, "gram_stain": 0.9, "sporulation": 0.0, "motility": 0.875, "range_salinity": 1.0, "facultative_respiration": 0.5, "anaerobic_respiration": 0.1, "aerobic_respiration": 0.4, "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", "rustica" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }