{ "type": "genome", "identifier": "GCF_018343695.1", "organism": "Lederbergia citrisecunda", "title": "Lederbergia citrisecunda", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Fujian Academy of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_018343695.1", "bioproject": "PRJNA224116", "biosample": "SAMN19008743", "wgs_master": "JAGYPJ000000000.1", "refseq_category": "reference genome", "taxid": "2833583", "species_taxid": "2833583", "organism_name": "Lederbergia citrisecunda", "infraspecific_name": "strain=FJAT-49732", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/11", "asm_name": "ASM1834369v1", "asm_submitter": "Fujian Academy of Agricultural Sciences", "gbrs_paired_asm": "GCA_018343695.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/343/695/GCF_018343695.1_ASM1834369v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4729684", "genome_size_ungapped": "4729614", "gc_percent": "36.500000", "replicon_count": "0", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_018343695.1-RS_2024_06_17", "annotation_date": "2024-06-17", "total_gene_count": "4646", "protein_coding_gene_count": "4498", "non_coding_gene_count": "104", "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 citrisecunda" ], "sample_taxid": [ "2833583" ], "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": "1.333 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4729684", "Number of Sequences": "4", "Longest Sequences (bp)": "4542774", "N50 (bp)": "4542774", "Gap Ratio (%)": "0.001480", "GCcontent (%)": "36.7", "Number of CDSs": "4602", "Average Protein Length": "285.8", "Coding Ratio (%)": "83.4", "Number of rRNAs": "21", "Number of tRNAs": "77", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Lederbergia citrisecundus", "strain": "strain=FJAT-49732", "accession": "GCA_018343695.1", "taxid": 2833583, "species_taxid": 2833583, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1572, "total_fragments": 1574, "ani_threshold": 95, "status": "conclusive" }, { "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": 84.7711, "matched_fragments": 1168, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lederbergia citri", "strain": "strain=FJAT-49780", "accession": "GCA_018343625.1", "taxid": 2833580, "species_taxid": 2833580, "relation_to_type": "type", "validated": true, "ani": 83.5539, "matched_fragments": 1091, "total_fragments": 1574, "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": 81.9685, "matched_fragments": 925, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus methanolicus", "strain": "strain=PB1", "accession": "GCA_000262755.1", "taxid": 1471, "species_taxid": 1471, "relation_to_type": "suspected-type", "validated": true, "ani": 78.9243, "matched_fragments": 64, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alkalihalobacillus krulwichiae", "strain": "strain=AM31D", "accession": "GCA_002109385.1", "taxid": 199441, "species_taxid": 199441, "relation_to_type": "type", "validated": true, "ani": 78.7761, "matched_fragments": 56, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacillus niameyensis", "strain": "strain=SIT3", "accession": "GCA_001375535.1", "taxid": 1522308, "species_taxid": 1522308, "relation_to_type": "type", "validated": true, "ani": 77.6679, "matched_fragments": 221, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Heyndrickxia sporothermodurans", "strain": "strain=DSM 10599", "accession": "GCA_016785185.1", "taxid": 46224, "species_taxid": 46224, "relation_to_type": "type", "validated": true, "ani": 77.257, "matched_fragments": 114, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siminovitchia fortis", "strain": "strain=DSM 16012", "accession": "GCA_003605365.2", "taxid": 254758, "species_taxid": 254758, "relation_to_type": "type", "validated": true, "ani": 77.1217, "matched_fragments": 98, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Lederbergia galactosidilytica", "strain": "strain=DSM 15595", "accession": "GCA_017873565.1", "taxid": 217031, "species_taxid": 217031, "relation_to_type": "type", "validated": true, "ani": 77.0721, "matched_fragments": 182, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neobacillus cucumis", "strain": "strain=DSM 101566", "accession": "GCA_016908975.1", "taxid": 1740721, "species_taxid": 1740721, "relation_to_type": "type", "validated": true, "ani": 76.8481, "matched_fragments": 102, "total_fragments": 1574, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_018343695.1", "gtdb_species": "s__FJAT-49711 sp018343695", "ani": 100.0, "matched_fragments": 1570, "total_fragments": 1574, "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_018343625.1", "gtdb_species": "s__FJAT-49711 sp018343625", "ani": 83.5183, "matched_fragments": 1094, "total_fragments": 1574, "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": 81.8848, "matched_fragments": 982, "total_fragments": 1574, "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_002019665.1", "gtdb_species": "s__Sutcliffiella_A halmapala", "ani": 79.0591, "matched_fragments": 73, "total_fragments": 1574, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_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_018343525.1", "gtdb_species": "s__FJAT-49754 sp018343525", "ani": 78.5871, "matched_fragments": 389, "total_fragments": 1574, "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_018343615.1", "gtdb_species": "s__Margalitia sp018343615", "ani": 78.5139, "matched_fragments": 126, "total_fragments": 1574, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia", "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_001420715.1", "gtdb_species": "s__Margalitia shackletonii", "ani": 78.1985, "matched_fragments": 147, "total_fragments": 1574, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Margalitia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003605405.2", "gtdb_species": "s__Siminovitchia terrae", "ani": 77.7367, "matched_fragments": 128, "total_fragments": 1574, "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": "99.14", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001375535.1", "gtdb_species": "s__Lederbergia niameyensis", "ani": 77.7302, "matched_fragments": 226, "total_fragments": 1574, "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": "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_007679095.1", "gtdb_species": "s__DE0126 sp007679095", "ani": 77.4147, "matched_fragments": 206, "total_fragments": 1574, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__DE0126", "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_002272245.1", "gtdb_species": "s__Neobacillus sp002272245", "ani": 77.3012, "matched_fragments": 79, "total_fragments": 1574, "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": "97.06", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017355205.1", "gtdb_species": "s__Lederbergia sp017355205", "ani": 77.1992, "matched_fragments": 175, "total_fragments": 1574, "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": "95.07", "min_intra_species_ani": "95.07", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007830235.1", "gtdb_species": "s__Cytobacillus oceanisediminis", "ani": 77.1862, "matched_fragments": 79, "total_fragments": 1574, "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_000518885.1", "gtdb_species": "s__Cytobacillus sp000518885", "ani": 77.151, "matched_fragments": 78, "total_fragments": 1574, "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": 77.0798, "matched_fragments": 184, "total_fragments": 1574, "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_003966145.1", "gtdb_species": "s__Ureibacillus telephonicus", "ani": 76.7378, "matched_fragments": 64, "total_fragments": 1574, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus", "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": "-" } ] }, "_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", "citrisecunda" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }