{ "type": "genome", "identifier": "GCF_900452975.1", "organism": "Listeria fleischmannii subsp. coloradonensis", "title": "Listeria fleischmannii subsp. coloradonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900452975.1", "bioproject": "PRJNA224116", "biosample": "SAMEA104307695", "wgs_master": "UGPD00000000.1", "refseq_category": "na", "taxid": "1081736", "species_taxid": "1069827", "organism_name": "Listeria fleischmannii subsp. coloradonensis", "infraspecific_name": "strain=NCTC13938", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "58116_E02", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900452975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/452/975/GCF_900452975.1_58116_E02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2875465", "genome_size_ungapped": "2875465", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900452975.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "2874", "protein_coding_gene_count": "2671", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Listeria fleischmannii subsp. coloradonensis" ], "sample_taxid": [ "1081736" ], "sample_host_organism": [ "environmental" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Northern Colorado" ], "sample_host_location_id": [], "data_size": "0.814 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)": "2875465", "Number of Sequences": "5", "Longest Sequences (bp)": "1978099", "N50 (bp)": "1978099", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.7", "Number of CDSs": "2887", "Average Protein Length": "292.9", "Coding Ratio (%)": "88.2", "Number of rRNAs": "16", "Number of tRNAs": "60", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 956, "total_fragments": 956, "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": 99.5275, "matched_fragments": 733, "total_fragments": 956, "ani_threshold": 95, "status": "conclusive" }, { "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": 95.8018, "matched_fragments": 842, "total_fragments": 956, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Listeria goaensis", "strain": "strain=ILCC801", "accession": "GCA_900186125.1", "taxid": 1649188, "species_taxid": 1649188, "relation_to_type": "type", "validated": true, "ani": 82.4766, "matched_fragments": 638, "total_fragments": 956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria floridensis", "strain": "strain=FSL S10-1187", "accession": "GCA_000525875.1", "taxid": 1494962, "species_taxid": 1494962, "relation_to_type": "type", "validated": true, "ani": 78.2255, "matched_fragments": 229, "total_fragments": 956, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Listeria aquatica", "strain": "strain=FSL S10-1188", "accession": "GCA_000525795.1", "taxid": 1494960, "species_taxid": 1494960, "relation_to_type": "type", "validated": true, "ani": 77.9484, "matched_fragments": 232, "total_fragments": 956, "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": 77.8862, "matched_fragments": 197, "total_fragments": 956, "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": 77.4964, "matched_fragments": 110, "total_fragments": 956, "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": 95.8018, "matched_fragments": 842, "total_fragments": 956, "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": 82.4973, "matched_fragments": 636, "total_fragments": 956, "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_000060285.1", "gtdb_species": "s__Listeria welshimeri", "ani": 79.113, "matched_fragments": 202, "total_fragments": 956, "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_000763495.1", "gtdb_species": "s__Listeria londoniensis", "ani": 78.571, "matched_fragments": 210, "total_fragments": 956, "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_011800755.1", "gtdb_species": "s__Listeria valentina", "ani": 78.3301, "matched_fragments": 207, "total_fragments": 956, "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_000525875.1", "gtdb_species": "s__Listeria floridensis", "ani": 78.24, "matched_fragments": 227, "total_fragments": 956, "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_003369925.1", "gtdb_species": "s__Listeria kieliensis_A", "ani": 78.2255, "matched_fragments": 225, "total_fragments": 956, "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_014229095.1", "gtdb_species": "s__Listeria cayugensis", "ani": 78.1654, "matched_fragments": 201, "total_fragments": 956, "gtdb_taxonomy": 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