{ "type": "genome", "identifier": "GCF_014773485.1", "organism": "Erwinia aphidicola", "title": "Erwinia aphidicola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Center for Disease Control and Prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014773485.1", "bioproject": "PRJNA224116", "biosample": "SAMN16130814", "wgs_master": "JACXBP000000000.1", "refseq_category": "na", "taxid": "68334", "species_taxid": "68334", "organism_name": "Erwinia aphidicola", "infraspecific_name": "strain=JCM 21238", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/21", "asm_name": "ASM1477348v1", "asm_submitter": "Chinese Center for Disease Control and Prevention", "gbrs_paired_asm": "GCA_014773485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/773/485/GCF_014773485.1_ASM1477348v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5118043", "genome_size_ungapped": "5118043", "gc_percent": "56.500000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014773485.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "4754", "protein_coding_gene_count": "4586", "non_coding_gene_count": "101", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-21", "dateModified": "2020-09-21", "datePublished": "2020-09-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Erwinia aphidicola" ], "sample_taxid": [ "68334" ], "sample_host_organism": [ "pea aphid" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan" ], "sample_host_location_id": [], "data_size": "1.440 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 8.33, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5118043", "Number of Sequences": "25", "Longest Sequences (bp)": "961531", "N50 (bp)": "575283", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "56.7", "Number of CDSs": "4682", "Average Protein Length": "318.5", "Coding Ratio (%)": "87.4", "Number of rRNAs": "7", "Number of tRNAs": "79", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Erwinia aphidicola", "strain": "strain=JCM 21238", "accession": "GCA_014773485.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1634, "total_fragments": 1691, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=X001", "accession": "GCA_024169515.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 98.13, "matched_fragments": 1440, "total_fragments": 1691, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Erwinia persicina", "strain": "strain=NBRC 102418", "accession": "GCA_001571305.1", "taxid": 55211, "species_taxid": 55211, "relation_to_type": "type", "validated": true, "ani": 83.2632, "matched_fragments": 1075, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia pyrifoliae", "strain": "strain=DSM 12163", "accession": "GCA_000026985.1", "taxid": 79967, "species_taxid": 79967, "relation_to_type": "type", "validated": true, "ani": 82.1142, "matched_fragments": 820, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia tasmaniensis", "strain": "strain=Et1/99", "accession": "GCA_000026185.1", "taxid": 338565, "species_taxid": 338565, "relation_to_type": "type", "validated": true, "ani": 81.8992, "matched_fragments": 850, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia amylovora", "strain": "strain=NBRC 12687", "accession": "GCA_000696075.1", "taxid": 552, "species_taxid": 552, "relation_to_type": "type", "validated": true, "ani": 81.8395, "matched_fragments": 810, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia amylovora", "strain": "strain=ATCC 15580", "accession": "GCA_017161565.1", "taxid": 552, "species_taxid": 552, "relation_to_type": "type", "validated": true, "ani": 81.8159, "matched_fragments": 817, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia piriflorinigrans", "strain": "strain=CFBP 5888", "accession": "GCA_001050515.1", "taxid": 665097, "species_taxid": 665097, "relation_to_type": "type", "validated": true, "ani": 81.7535, "matched_fragments": 809, "total_fragments": 1691, "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": 80.5281, "matched_fragments": 797, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mixta gaviniae", "strain": "strain=DSM 22758", "accession": "GCA_002953195.1", "taxid": 665914, "species_taxid": 665914, "relation_to_type": "type", "validated": true, "ani": 80.1379, "matched_fragments": 797, "total_fragments": 1691, "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": 79.8261, "matched_fragments": 774, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia entomophila", "strain": "strain=A1", "accession": "GCA_021462285.1", "taxid": 42906, "species_taxid": 42906, "relation_to_type": "type", "validated": true, "ani": 79.2729, "matched_fragments": 671, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leclercia pneumoniae", "strain": "strain=49125", "accession": "GCA_018987305.1", "taxid": 2815358, "species_taxid": 2815358, "relation_to_type": "type", "validated": true, "ani": 78.8505, "matched_fragments": 518, "total_fragments": 1691, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 8.33, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_014773485.1", "gtdb_species": "s__Erwinia aphidicola", "ani": 100.0, "matched_fragments": 1631, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.08", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_001756855.1", "gtdb_species": "s__Erwinia dacicola", "ani": 92.8034, "matched_fragments": 365, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.66", "min_intra_species_af": "0.61", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014838825.1", "gtdb_species": "s__Erwinia persicina_A", "ani": 83.534, "matched_fragments": 1102, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "99.46", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_012271765.1", "gtdb_species": "s__Erwinia rhapontici", "ani": 83.4635, "matched_fragments": 1116, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "96.56", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001571305.1", "gtdb_species": "s__Erwinia persicina", "ani": 83.2535, "matched_fragments": 1076, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.41", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_009738185.1", "gtdb_species": "s__Erwinia sp009738185", "ani": 83.0631, "matched_fragments": 1067, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.50", "min_intra_species_ani": "99.50", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018141005.1", "gtdb_species": "s__Erwinia sp001422605", "ani": 82.9317, "matched_fragments": 1010, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "98.36", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016909495.1", "gtdb_species": "s__Erwinia coffeiphila", "ani": 82.6398, "matched_fragments": 963, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.75", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000026985.1", "gtdb_species": "s__Erwinia pyrifoliae", "ani": 82.0826, "matched_fragments": 824, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001050515.1", "gtdb_species": "s__Erwinia piriflorinigrans", "ani": 81.749, "matched_fragments": 810, "total_fragments": 1691, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "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": 81.3782, "matched_fragments": 949, "total_fragments": 1691, "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": -0.155, "cell_length": 0.301, "doubling_h": 0.093, "growth_tmp": 30.0, "optimum_tmp": 28.613, "optimum_ph": null, "genome_size": 4704408.66, "gc_content": 52.638, "coding_genes": 4041.125, "rRNA16S_genes": 7.0, "tRNA_genes": 78.416, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "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": [ "Erwinia", "aphidicola" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }