{ "type": "genome", "identifier": "GCF_006494375.1", "organism": "Pantoea anthophila", "title": "Pantoea anthophila", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ottawa Research and Development Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006494375.1", "bioproject": "PRJNA224116", "biosample": "SAMN12097134", "wgs_master": "VHIZ00000000.1", "refseq_category": "na", "taxid": "470931", "species_taxid": "470931", "organism_name": "Pantoea anthophila", "infraspecific_name": "strain=LMG 2558", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/26", "asm_name": "ASM649437v1", "asm_submitter": "Ottawa Research and Development Center", "gbrs_paired_asm": "GCA_006494375.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/494/375/GCF_006494375.1_ASM649437v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4699058", "genome_size_ungapped": "4699058", "gc_percent": "57.000000", "replicon_count": "0", "scaffold_count": "66", "contig_count": "66", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006494375.1-RS_2024_09_08", "annotation_date": "2024-09-08", "total_gene_count": "4434", "protein_coding_gene_count": "4271", "non_coding_gene_count": "106", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-26", "dateModified": "2019-06-26", "datePublished": "2019-06-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Pantoea anthophila" ], "sample_taxid": [ "470931" ], "sample_host_organism": [ "Impatiens balsamina" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.326 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)": "4699058", "Number of Sequences": "66", "Longest Sequences (bp)": "541255", "N50 (bp)": "238228", "Gap Ratio (%)": "0.000085", "GCcontent (%)": "56.8", "Number of CDSs": "4323", "Average Protein Length": "311.2", "Coding Ratio (%)": "85.9", "Number of rRNAs": "9", "Number of tRNAs": "76", "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": 88.6125, "matched_fragments": 1287, "total_fragments": 1537, "ani_threshold": 95, "status": "below_threshold" }, { "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": 88.6033, "matched_fragments": 1288, "total_fragments": 1537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea deleyi", "strain": "strain=LMG 24200", "accession": "GCA_006494415.1", "taxid": 470932, "species_taxid": 470932, "relation_to_type": "type", "validated": true, "ani": 87.6937, "matched_fragments": 1243, "total_fragments": 1537, "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": 87.6844, "matched_fragments": 1114, "total_fragments": 1537, "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": 87.5716, "matched_fragments": 1267, "total_fragments": 1537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea eucalypti", "strain": "strain=LMG 24197", "accession": "GCA_006494355.1", "taxid": 470933, "species_taxid": 470933, "relation_to_type": "type", "validated": true, "ani": 87.4699, "matched_fragments": 1262, "total_fragments": 1537, "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": 87.4402, "matched_fragments": 1279, "total_fragments": 1537, "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": 85.5888, "matched_fragments": 1096, "total_fragments": 1537, "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": 81.0848, "matched_fragments": 835, "total_fragments": 1537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=X001", "accession": "GCA_024169515.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 79.7795, "matched_fragments": 732, "total_fragments": 1537, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia phyllosphaerae", "strain": "strain=CMYE1", "accession": "GCA_019132875.1", "taxid": 2853256, "species_taxid": 2853256, "relation_to_type": "type", "validated": true, "ani": 79.207, "matched_fragments": 634, "total_fragments": 1537, "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": 78.539, "matched_fragments": 488, "total_fragments": 1537, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006494375.1", "gtdb_species": "s__Pantoea anthophila", "ani": 100.0, "matched_fragments": 1535, "total_fragments": 1537, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "98.21", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 16, "status": "conclusive" }, { "accession": "GCF_001598475.1", "gtdb_species": "s__Pantoea agglomerans", "ani": 88.6033, "matched_fragments": 1288, "total_fragments": 1537, "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": "-" }, { "accession": "GCF_008632075.1", "gtdb_species": "s__Pantoea sp008632075", "ani": 88.4452, "matched_fragments": 1276, "total_fragments": 1537, "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": "-" }, { "accession": "GCF_004792415.1", "gtdb_species": "s__Pantoea vagans", "ani": 88.4443, "matched_fragments": 1307, "total_fragments": 1537, "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_009905795.1", "gtdb_species": "s__Pantoea sp003512445", "ani": 88.1223, "matched_fragments": 1265, "total_fragments": 1537, "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_900115075.1", "gtdb_species": "s__Pantoea sp900115075", "ani": 88.1084, "matched_fragments": 1309, "total_fragments": 1537, "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_006494415.1", "gtdb_species": "s__Pantoea deleyi", "ani": 87.6883, "matched_fragments": 1244, "total_fragments": 1537, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009646115.1", "gtdb_species": "s__Pantoea eucalypti", "ani": 87.4492, "matched_fragments": 1278, "total_fragments": 1537, "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_003236715.1", "gtdb_species": "s__Pantoea sp003236715", "ani": 87.3213, "matched_fragments": 1165, "total_fragments": 1537, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea", "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_000196615.1", "gtdb_species": "s__Erwinia billingiae", "ani": 79.6796, "matched_fragments": 733, "total_fragments": 1537, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "97.43", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 7, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.046, "cell_length": 0.079, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 33.875, "optimum_ph": null, "genome_size": 4600679.0, "gc_content": 53.712, "coding_genes": 3801.881, "rRNA16S_genes": 6.428, "tRNA_genes": 74.931, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pantoea", "anthophila" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }