{ "type": "genome", "identifier": "GCF_018343625.1", "organism": "Lederbergia citri", "title": "Lederbergia citri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Fujian Academy of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018343625.1", "bioproject": "PRJNA224116", "biosample": "SAMN19008746", "wgs_master": "JAGYPG000000000.1", "refseq_category": "reference genome", "taxid": "2833580", "species_taxid": "2833580", "organism_name": "Lederbergia citri", "infraspecific_name": "strain=FJAT-49780", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/11", "asm_name": "ASM1834362v1", "asm_submitter": "Fujian Academy of Agricultural Sciences", "gbrs_paired_asm": "GCA_018343625.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/343/625/GCF_018343625.1_ASM1834362v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4823521", "genome_size_ungapped": "4823421", "gc_percent": "37.000000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "9", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018343625.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4802", "protein_coding_gene_count": "4625", "non_coding_gene_count": "101", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-11", "dateModified": "2021-05-11", "datePublished": "2021-05-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Lederbergia citri" ], "sample_taxid": [ "2833580" ], "sample_host_organism": [ "citrus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Zhangzhou" ], "sample_host_location_id": [], "data_size": "1.362 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)": "4823521", "Number of Sequences": "9", "Longest Sequences (bp)": "1695390", "N50 (bp)": "1559369", "Gap Ratio (%)": "0.002073", "GCcontent (%)": "37.1", "Number of CDSs": "4766", "Average Protein Length": "283.0", "Coding Ratio (%)": "83.9", "Number of rRNAs": "10", "Number of tRNAs": "78", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lederbergia citri", "strain": "strain=FJAT-49780", "accession": "GCA_018343625.1", "taxid": 2833580, "species_taxid": 2833580, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1603, "total_fragments": 1604, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Lederbergia citrisecundus", "strain": "strain=FJAT-49732", "accession": "GCA_018343695.1", "taxid": 2833583, "species_taxid": 2833583, "relation_to_type": "type", "validated": true, "ani": 83.6321, "matched_fragments": 1100, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lederbergia wuyishanensis", "strain": "strain=CGMCC 1.12709", "accession": "GCA_022900255.1", "taxid": 1347903, "species_taxid": 1347903, "relation_to_type": "type", "validated": true, "ani": 82.9323, "matched_fragments": 1075, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lederbergia panacisoli", "strain": "strain=KACC 17503", "accession": "GCA_024626525.1", "taxid": 1255251, "species_taxid": 1255251, "relation_to_type": "type", "validated": true, "ani": 81.7915, "matched_fragments": 896, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus licheniformis", "strain": "strain=DSM 13", "accession": "GCA_022630555.1", "taxid": 1402, "species_taxid": 1402, "relation_to_type": "type", "validated": true, "ani": 77.8559, "matched_fragments": 52, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Heyndrickxia oleronia", "strain": "strain=DSM 9356", "accession": "GCA_025263665.1", "taxid": 38875, "species_taxid": 38875, "relation_to_type": "type", "validated": true, "ani": 77.7468, "matched_fragments": 141, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Domibacillus aminovorans", "strain": "strain=DSM 1314", "accession": "GCA_001643235.1", "taxid": 29332, "species_taxid": 29332, "relation_to_type": "type", "validated": true, "ani": 77.5946, "matched_fragments": 58, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Litchfieldia salsa", "strain": "strain=IBRC-M10078", "accession": "GCA_900104555.1", "taxid": 930152, "species_taxid": 930152, "relation_to_type": "type", "validated": true, "ani": 76.7437, "matched_fragments": 75, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Domibacillus mangrovi", "strain": "strain=SAOS 44", "accession": "GCA_001906925.1", "taxid": 1714354, "species_taxid": 1714354, "relation_to_type": "type", "validated": true, "ani": 76.4516, "matched_fragments": 50, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lysinibacillus macroides", "strain": "strain=DSM 54", "accession": "GCA_001281525.1", "taxid": 33935, "species_taxid": 33935, "relation_to_type": "type", "validated": true, "ani": 76.4052, "matched_fragments": 51, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Priestia megaterium", "strain": "strain=NBRC 15308", "accession": "GCA_001591525.1", "taxid": 1404, "species_taxid": 1404, "relation_to_type": "type", "validated": true, "ani": 76.3231, "matched_fragments": 67, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neobacillus fumarioli", "strain": "strain=NBRC 102428", "accession": "GCA_001591485.1", "taxid": 105229, "species_taxid": 105229, "relation_to_type": "type", "validated": true, "ani": 76.1963, "matched_fragments": 61, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018343625.1", "gtdb_species": "s__FJAT-49711 sp018343625", "ani": 100.0, "matched_fragments": 1603, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711", "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_018343695.1", "gtdb_species": "s__FJAT-49711 sp018343695", "ani": 83.6453, "matched_fragments": 1099, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711", "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_018343715.1", "gtdb_species": "s__FJAT-49711 sp018343715", "ani": 81.4931, "matched_fragments": 975, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711", "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_900199725.1", "gtdb_species": "s__Cytobacillus massiliigabonensis", "ani": 78.3324, "matched_fragments": 95, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_018343525.1", "gtdb_species": "s__FJAT-49754 sp018343525", "ani": 78.3115, "matched_fragments": 376, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49754", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018343515.1", "gtdb_species": "s__Bacillus_AH sp018343515", "ani": 77.9493, "matched_fragments": 215, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH", "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_000374565.1", "gtdb_species": "s__Siminovitchia fordii", "ani": 77.6528, "matched_fragments": 123, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001643235.1", "gtdb_species": "s__Domibacillus aminovorans", "ani": 77.5946, "matched_fragments": 58, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.53", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_008764245.1", "gtdb_species": "s__Lederbergia ruris", "ani": 77.359, "matched_fragments": 178, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "98.48", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003182355.1", "gtdb_species": "s__Cytobacillus oceanisediminis_A", "ani": 77.2515, "matched_fragments": 68, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus", "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_017873565.1", "gtdb_species": "s__Lederbergia galactosidilytica", "ani": 76.9605, "matched_fragments": 201, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.18", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002860285.1", "gtdb_species": "s__Peribacillus_A sp002860285", "ani": 76.646, "matched_fragments": 70, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus_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_001906925.1", "gtdb_species": "s__Domibacillus mangrovi", "ani": 76.5351, "matched_fragments": 50, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus", "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": "GCA_011524565.1", "gtdb_species": "s__Niallia sp011524565", "ani": 76.2014, "matched_fragments": 62, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia", "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_001591485.1", "gtdb_species": "s__Neobacillus fumarioli", "ani": 76.1963, "matched_fragments": 61, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus", "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_001757995.1", "gtdb_species": "s__Bacillus_A mycoides_B", "ani": 76.0678, "matched_fragments": 74, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.86", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001076885.1", "gtdb_species": "s__Niallia sp001076885", "ani": 75.9723, "matched_fragments": 73, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Niallia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.59", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "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": [ "Lederbergia", "citri" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }