{ "type": "genome", "identifier": "GCF_000344175.1", "organism": "Listeria fleischmannii subsp. fleischmannii LU2006-1", "title": "Listeria fleischmannii subsp. fleischmannii LU2006-1", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Cornell University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000344175.1", "bioproject": "PRJNA224116", "biosample": "SAMN02415229", "wgs_master": "ALWW00000000.1", "refseq_category": "na", "taxid": "1214117", "species_taxid": "1069827", "organism_name": "Listeria fleischmannii subsp. fleischmannii LU2006-1", "infraspecific_name": "strain=LU2006-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/03/04", "asm_name": "ASM34417v1", "asm_submitter": "Cornell University", "gbrs_paired_asm": "GCA_000344175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/344/175/GCF_000344175.1_ASM34417v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2841134", "genome_size_ungapped": "2841134", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "102", "contig_count": "102", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000344175.1-RS_2024_04_02", "annotation_date": "2024-04-02", "total_gene_count": "2988", "protein_coding_gene_count": "2611", "non_coding_gene_count": "90", "pubmed_id": "23524352" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-03-04", "dateModified": "2013-03-04", "datePublished": "2013-03-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Listeria fleischmannii subsp. fleischmannii LU2006-1" ], "sample_taxid": [ "1214117" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Switzerland" ], "sample_host_location_id": [], "data_size": "0.808 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)": "2841134", "Number of Sequences": "102", "Longest Sequences (bp)": "148496", "N50 (bp)": "48159", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.3", "Number of CDSs": "3041", "Average Protein Length": "270.5", "Coding Ratio (%)": "86.8", "Number of rRNAs": "8", "Number of tRNAs": "66", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Listeria fleischmannii subsp. fleischmannii", "strain": "strain=LU2006-1", "accession": "GCA_000344175.1", "taxid": 1671902, "species_taxid": 1069827, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 899, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria fleischmannii subsp. coloradonensis", "strain": "strain=NCTC13938", "accession": "GCA_900452975.1", "taxid": 1081736, "species_taxid": 1069827, "relation_to_type": "type", "validated": true, "ani": 95.874, "matched_fragments": 847, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria fleischmannii subsp. coloradonensis", "strain": "strain=TTU M1-001", "accession": "GCA_000252625.2", "taxid": 1081736, "species_taxid": 1069827, "relation_to_type": "type", "validated": true, "ani": 95.5165, "matched_fragments": 673, "total_fragments": 902, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria goaensis", "strain": "strain=ILCC801", "accession": "GCA_900186125.1", "taxid": 1649188, 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"validated": true, "ani": 77.911, "matched_fragments": 185, "total_fragments": 902, "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": 77.8321, "matched_fragments": 209, "total_fragments": 902, "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": 77.3726, "matched_fragments": 124, "total_fragments": 902, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000344175.1", "gtdb_species": "s__Listeria fleischmannii", "ani": 100.0, "matched_fragments": 899, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.87", "min_intra_species_ani": "95.72", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 9, "status": "conclusive" }, { "accession": "GCF_900186125.1", "gtdb_species": "s__Listeria goaensis", "ani": 82.5979, "matched_fragments": 615, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.37", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_000525875.1", "gtdb_species": "s__Listeria floridensis", "ani": 78.2857, "matched_fragments": 219, "total_fragments": 902, "gtdb_taxonomy": 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"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_003369925.1", "gtdb_species": "s__Listeria kieliensis_A", "ani": 78.1752, "matched_fragments": 218, "total_fragments": 902, "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": "99.04", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000525795.1", "gtdb_species": "s__Listeria aquatica", "ani": 78.1059, "matched_fragments": 217, "total_fragments": 902, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.71", "min_intra_species_ani": "97.71", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000763495.1", "gtdb_species": "s__Listeria londoniensis", "ani": 78.0317, "matched_fragments": 202, "total_fragments": 902, "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": "-" }, { "accession": "GCF_900183385.1", "gtdb_species": "s__Listeria costaricensis", "ani": 77.989, "matched_fragments": 169, "total_fragments": 902, "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_014229645.1", "gtdb_species": "s__Listeria sp014229645", "ani": 77.9295, "matched_fragments": 196, "total_fragments": 902, "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_014322765.1", "gtdb_species": "s__Listeria immobilis", "ani": 77.911, "matched_fragments": 185, "total_fragments": 902, "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": "-" }, { 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77.5179, "matched_fragments": 120, "total_fragments": 902, "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_000525975.1", "gtdb_species": "s__Listeria_A rocourtiae", "ani": 77.3726, "matched_fragments": 124, "total_fragments": 902, "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", "fleischmannii", "subsp.", "fleischmannii", "LU2006-1" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }