{ "type": "genome", "identifier": "GCF_001436255.1", "organism": "Lentilactobacillus rapi DSM 19907 = JCM 15042", "title": "Lentilactobacillus rapi DSM 19907 = JCM 15042", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shanghai Majorbio", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001436255.1", "bioproject": "PRJNA224116", "biosample": "SAMN02369472", "wgs_master": "AZEI00000000.1", "refseq_category": "reference genome", "taxid": "1423795", "species_taxid": "481723", "organism_name": "Lentilactobacillus rapi DSM 19907 = JCM 15042", "infraspecific_name": "strain=DSM 19907", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/11/06", "asm_name": "ASM143625v1", "asm_submitter": "Shanghai Majorbio", "gbrs_paired_asm": "GCA_001436255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/436/255/GCF_001436255.1_ASM143625v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2854844", "genome_size_ungapped": "2854474", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "87", "contig_count": "87", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001436255.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2701", "protein_coding_gene_count": "2595", "non_coding_gene_count": "62", "pubmed_id": "26415554" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-11-06", "dateModified": "2015-11-06", "datePublished": "2015-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Lentilactobacillus rapi DSM 19907 = JCM 15042" ], "sample_taxid": [ "1423795" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "0.816 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)": "2854844", "Number of Sequences": "87", "Longest Sequences (bp)": "533768", "N50 (bp)": "72132", "Gap Ratio (%)": "0.012960", "GCcontent (%)": "42.9", "Number of CDSs": "2649", "Average Protein Length": "302.9", "Coding Ratio (%)": "84.3", "Number of rRNAs": "2", "Number of tRNAs": "56", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lentilactobacillus rapi subsp. rapi", "strain": "strain=DSM 19907", "accession": "GCA_001436255.1", "taxid": 2944812, "species_taxid": 481723, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 912, "total_fragments": 912, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lentilactobacillus rapi subsp. rapi", "strain": "strain=JCM 15042", "accession": "GCA_001311445.1", "taxid": 2944812, "species_taxid": 481723, "relation_to_type": "type", "validated": true, "ani": 99.8687, "matched_fragments": 869, "total_fragments": 912, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lentilactobacillus kisonensis", "strain": "strain=JCM 15041", "accession": "GCA_001311425.1", "taxid": 481722, "species_taxid": 481722, "relation_to_type": "type", "validated": true, "ani": 80.8858, "matched_fragments": 479, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus kisonensis", "strain": "strain=DSM 19906", "accession": "GCA_001434135.1", "taxid": 481722, "species_taxid": 481722, "relation_to_type": "type", "validated": true, "ani": 80.8247, "matched_fragments": 477, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus fungorum", "strain": "strain=YK48G", "accession": "GCA_016860605.1", "taxid": 2201250, "species_taxid": 2201250, "relation_to_type": "type", "validated": true, "ani": 79.498, "matched_fragments": 410, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus otakiensis", "strain": "strain=DSM 19908", "accession": "GCA_001434145.1", "taxid": 481720, "species_taxid": 481720, "relation_to_type": "type", "validated": true, "ani": 79.1985, "matched_fragments": 277, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus otakiensis", "strain": "strain=JCM 15040", "accession": "GCA_000415925.1", "taxid": 481720, "species_taxid": 481720, "relation_to_type": "type", "validated": true, "ani": 79.1325, "matched_fragments": 284, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus otakiensis", "strain": "strain=JCM 15040", "accession": "GCA_001311395.1", "taxid": 481720, "species_taxid": 481720, "relation_to_type": "type", "validated": true, "ani": 79.1166, "matched_fragments": 279, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lentilactobacillus kefiri", "strain": "strain=NBRC 15888", "accession": "GCA_007989105.1", "taxid": 33962, "species_taxid": 33962, "relation_to_type": "type", "validated": true, "ani": 79.1145, "matched_fragments": 255, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Secundilactobacillus angelensis", "strain": "strain=HBUAS51383", "accession": "GCA_012641075.1", "taxid": 2722706, "species_taxid": 2722706, "relation_to_type": "type", "validated": true, "ani": 77.4976, "matched_fragments": 66, "total_fragments": 912, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001436255.1", "gtdb_species": "s__Lentilactobacillus rapi", "ani": 99.9999, "matched_fragments": 912, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.89", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_019061365.1", "gtdb_species": "s__Lentilactobacillus sp019061365", "ani": 93.609, "matched_fragments": 690, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001434135.1", "gtdb_species": "s__Lentilactobacillus kisonensis", "ani": 80.8592, "matched_fragments": 474, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.70", "min_intra_species_ani": "99.52", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016860605.1", "gtdb_species": "s__Lentilactobacillus sp016860605", "ani": 79.5032, "matched_fragments": 410, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "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_001434145.1", "gtdb_species": "s__Lentilactobacillus otakiensis", "ani": 79.2155, "matched_fragments": 276, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.91", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_007989105.1", "gtdb_species": "s__Lentilactobacillus kefiri", "ani": 79.1145, "matched_fragments": 255, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.76", "min_intra_species_ani": "99.64", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001435575.1", "gtdb_species": "s__Lentilactobacillus sunkii", "ani": 78.8304, "matched_fragments": 254, "total_fragments": 912, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.44", "min_intra_species_ani": "96.44", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Lentilactobacillus", "rapi", "DSM", "19907", "=", "JCM", "15042" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }