{ "type": "genome", "identifier": "GCF_900637745.1", "organism": "Listeria ivanovii subsp. londoniensis", "title": "Listeria ivanovii subsp. londoniensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900637745.1", "bioproject": "PRJNA224116", "biosample": "SAMEA26389918", "wgs_master": "na", "refseq_category": "na", "taxid": "202752", "species_taxid": "1638", "organism_name": "Listeria ivanovii subsp. londoniensis", "infraspecific_name": "strain=NCTC12701", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/20", "asm_name": "52551_F01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900637745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/637/745/GCF_900637745.1_52551_F01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3007116", "genome_size_ungapped": "3007116", "gc_percent": "37.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-13", "total_gene_count": "2977", "protein_coding_gene_count": "2831", "non_coding_gene_count": "89", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-20", "dateModified": "2018-12-20", "datePublished": "2018-12-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Listeria ivanovii subsp. londoniensis" ], "sample_taxid": [ "202752" ], "sample_host_organism": [ "not available" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.845 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)": "3007116", "Number of Sequences": "1", "Longest Sequences (bp)": "3007116", "N50 (bp)": "3007116", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.0", "Number of CDSs": "2897", "Average Protein Length": "304.1", "Coding Ratio (%)": "87.9", "Number of rRNAs": "18", "Number of tRNAs": "67", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Listeria ivanovii subsp. ivanovii", "strain": "strain=NCTC11007", "accession": "GCA_900187195.1", "taxid": 202751, "species_taxid": 1638, "relation_to_type": "type", "validated": true, "ani": 93.4352, "matched_fragments": 869, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria ivanovii subsp. ivanovii", "strain": "strain=NCTC11846", "accession": "GCA_900187025.1", "taxid": 202751, "species_taxid": 1638, "relation_to_type": "type", "validated": true, "ani": 93.4346, "matched_fragments": 869, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria ivanovii subsp. ivanovii", "strain": "strain=WSLC 3010", "accession": "GCA_000763515.1", "taxid": 202751, "species_taxid": 1638, "relation_to_type": "type", "validated": true, "ani": 93.4238, "matched_fragments": 866, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria ivanovii subsp. ivanovii", "strain": "strain=PAM 55", "accession": "GCA_000252975.1", "taxid": 202751, "species_taxid": 1638, "relation_to_type": "claderef", "validated": true, "ani": 93.4211, "matched_fragments": 861, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria seeligeri", "strain": "strain=SLCC3954", "accession": "GCA_000027145.1", "taxid": 1640, "species_taxid": 1640, "relation_to_type": "type", "validated": true, "ani": 88.8536, "matched_fragments": 782, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria immobilis", "strain": "strain=FSL L7-1519", "accession": "GCA_014322765.1", "taxid": 2713502, "species_taxid": 2713502, "relation_to_type": "type", "validated": true, "ani": 88.0752, "matched_fragments": 796, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria innocua", "strain": "strain=F4078", "accession": "GCA_024721565.1", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "type", "validated": true, "ani": 84.2047, "matched_fragments": 714, "total_fragments": 1002, "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": 84.1131, "matched_fragments": 728, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria innocua", "strain": "strain=F4078", "accession": "GCA_014527425.1", "taxid": 1642, "species_taxid": 1642, "relation_to_type": "type", "validated": true, "ani": 84.0927, "matched_fragments": 718, "total_fragments": 1002, "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": 84.0344, "matched_fragments": 720, "total_fragments": 1002, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000763495.1", "gtdb_species": "s__Listeria londoniensis", "ani": 99.3571, "matched_fragments": 943, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.36", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 17, "status": "conclusive" }, { "accession": "GCF_900187025.1", "gtdb_species": "s__Listeria ivanovii", "ani": 93.4342, "matched_fragments": 869, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.75", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_000027145.1", "gtdb_species": "s__Listeria seeligeri", "ani": 88.8649, "matched_fragments": 783, "total_fragments": 1002, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.08", "min_intra_species_ani": "96.23", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 167, "status": "-" }, { "accession": "GCF_014322765.1", "gtdb_species": "s__Listeria immobilis", "ani": 88.0752, "matched_fragments": 796, "total_fragments": 1002, "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": "-" }, { "accession": "GCF_000307025.1", "gtdb_species": "s__Listeria monocytogenes_B", "ani": 84.1355, "matched_fragments": 731, "total_fragments": 1002, "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_014229645.1", "gtdb_species": "s__Listeria sp014229645", "ani": 84.0948, "matched_fragments": 694, "total_fragments": 1002, "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_900187225.1", "gtdb_species": "s__Listeria monocytogenes", "ani": 84.0105, "matched_fragments": 743, "total_fragments": 1002, "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_015276835.1", "gtdb_species": "s__Listeria innocua", "ani": 84.0072, "matched_fragments": 730, "total_fragments": 1002, "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": "-" }, { "accession": "GCF_014229095.1", "gtdb_species": "s__Listeria cayugensis", "ani": 83.9826, "matched_fragments": 693, "total_fragments": 1002, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.373, "cell_length": 0.255, "doubling_h": -0.172, "growth_tmp": 36.0, "optimum_tmp": 31.4, "optimum_ph": 6.75, "genome_size": 2955259.0, "gc_content": 37.005, "coding_genes": 2747.75, "rRNA16S_genes": 6.0, "tRNA_genes": 67.0, "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", "ivanovii", "subsp.", "londoniensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }