{ "type": "genome", "identifier": "GCF_003710245.1", "organism": "[Curtobacterium] plantarum", "title": "[Curtobacterium] plantarum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chunlab", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003710245.1", "bioproject": "PRJNA224116", "biosample": "SAMN10290473", "wgs_master": "RHDS00000000.1", "refseq_category": "reference genome", "taxid": "221276", "species_taxid": "221276", "organism_name": "[Curtobacterium] plantarum", "infraspecific_name": "strain=LMG 16222", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/11/04", "asm_name": "ASM371024v1", "asm_submitter": "Chunlab", "gbrs_paired_asm": "GCA_003710245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/710/245/GCF_003710245.1_ASM371024v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4981783", "genome_size_ungapped": "4981783", "gc_percent": "55.000000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003710245.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "4692", "protein_coding_gene_count": "4529", "non_coding_gene_count": "90", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-11-04", "dateModified": "2018-11-04", "datePublished": "2018-11-04", "_annotation": { "sample_count": 1, "sample_organism": [ "[Curtobacterium] plantarum" ], "sample_taxid": [ "221276" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.407 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)": "4981783", "Number of Sequences": "28", "Longest Sequences (bp)": "1020354", "N50 (bp)": "503616", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.1", "Number of CDSs": "4604", "Average Protein Length": "309.6", "Coding Ratio (%)": "85.8", "Number of rRNAs": "6", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pantoea agglomerans", "strain": "strain=FDAARGOS 1447", "accession": "GCA_019048385.1", "taxid": 549, "species_taxid": 549, "relation_to_type": "suspected-type", "validated": true, "ani": 98.4851, "matched_fragments": 1475, "total_fragments": 1646, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pantoea agglomerans", "strain": "strain=NBRC 102470", "accession": "GCA_001598475.1", "taxid": 549, "species_taxid": 549, "relation_to_type": "suspected-type", "validated": true, "ani": 98.445, "matched_fragments": 1479, "total_fragments": 1646, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pantoea eucalypti", "strain": "strain=LMG 24197", "accession": "GCA_006494355.1", "taxid": 470933, "species_taxid": 470933, "relation_to_type": "type", "validated": true, "ani": 90.6957, "matched_fragments": 1356, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea eucalypti", "strain": "strain=LMG 24197", "accession": "GCA_009646115.1", "taxid": 470933, "species_taxid": 470933, "relation_to_type": "type", "validated": true, "ani": 90.6483, "matched_fragments": 1397, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG 24200", "accession": "GCA_002095375.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 88.48, "matched_fragments": 1147, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG24200", "accession": "GCA_022647325.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 88.407, "matched_fragments": 1283, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea conspicua", "strain": "strain=LMG 24534", "accession": "GCA_002095315.1", "taxid": 472705, "species_taxid": 472705, "relation_to_type": "type", "validated": true, "ani": 86.5469, "matched_fragments": 1158, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea stewartii subsp. indologenes", "strain": "strain=LMG 2632", "accession": "GCA_000757405.2", "taxid": 66270, "species_taxid": 66269, "relation_to_type": "type", "validated": true, "ani": 80.8402, "matched_fragments": 885, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_001971035.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 78.6878, "matched_fragments": 467, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 78.6289, "matched_fragments": 515, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia nevei", "strain": "strain=S15", "accession": "GCA_008364245.1", "taxid": 2703794, "species_taxid": 2703794, "relation_to_type": "type", "validated": true, "ani": 78.5698, "matched_fragments": 498, "total_fragments": 1646, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001598475.1", "gtdb_species": "s__Pantoea agglomerans", "ani": 98.445, "matched_fragments": 1479, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "96.93", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 124, "status": "conclusive" }, { "accession": "GCF_900115075.1", "gtdb_species": "s__Pantoea sp900115075", "ani": 92.1782, "matched_fragments": 1427, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.06", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009905795.1", "gtdb_species": "s__Pantoea sp003512445", "ani": 91.5425, "matched_fragments": 1332, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.25", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013415305.1", "gtdb_species": "s__Pantoea sp002419935", "ani": 91.1837, "matched_fragments": 1352, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004792415.1", "gtdb_species": "s__Pantoea vagans", "ani": 91.1085, "matched_fragments": 1390, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.00", "min_intra_species_ani": "95.86", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_009646115.1", "gtdb_species": "s__Pantoea eucalypti", "ani": 90.6422, "matched_fragments": 1398, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_008632075.1", "gtdb_species": "s__Pantoea sp008632075", "ani": 90.6141, "matched_fragments": 1352, "total_fragments": 1646, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.47", "min_intra_species_ani": "99.36", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.94", "num_clustered_genomes": 34, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "[Curtobacterium]", "plantarum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }