{ "type": "genome", "identifier": "GCF_009738185.1", "organism": "Erwinia sorbitola", "title": "Erwinia sorbitola", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Center for Disease Control and Prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009738185.1", "bioproject": "PRJNA224116", "biosample": "SAMN13441016", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2681984", "species_taxid": "2681984", "organism_name": "Erwinia sorbitola", "infraspecific_name": "strain=J780", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/12/10", "asm_name": "ASM973818v1", "asm_submitter": "Chinese Center for Disease Control and Prevention", "gbrs_paired_asm": "GCA_009738185.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/738/185/GCF_009738185.1_ASM973818v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4750253", "genome_size_ungapped": "4750253", "gc_percent": "53.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009738185.1-RS_2024_09_13", "annotation_date": "2024-09-13", "total_gene_count": "4343", "protein_coding_gene_count": "4170", "non_coding_gene_count": "123", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-12-10", "dateModified": "2019-12-10", "datePublished": "2019-12-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Erwinia sorbitola" ], "sample_taxid": [ "2681984" ], "sample_host_organism": [ "ruddy shelduck" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Qinghai-Tibet Plateau" ], "sample_host_location_id": [], "data_size": "1.340 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)": "4750253", "Number of Sequences": "2", "Longest Sequences (bp)": "4699895", "N50 (bp)": "4699895", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.2", "Number of CDSs": "4231", "Average Protein Length": "324.4", "Coding Ratio (%)": "86.7", "Number of rRNAs": "22", "Number of tRNAs": "82", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Erwinia persicina", "strain": "strain=NBRC 102418", "accession": "GCA_001571305.1", "taxid": 55211, "species_taxid": 55211, "relation_to_type": "type", "validated": true, "ani": 83.862, "matched_fragments": 1104, "total_fragments": 1582, "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": 83.2106, "matched_fragments": 1058, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=JCM 21238", "accession": "GCA_014773485.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 83.0569, "matched_fragments": 1051, "total_fragments": 1582, "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": 81.5295, "matched_fragments": 752, "total_fragments": 1582, "ani_threshold": 95, "status": 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67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 78.6869, "matched_fragments": 461, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salmonella enterica subsp. enterica", "strain": "strain=PartC-Senterica-RM8376", "accession": "GCA_022869965.1", "taxid": 59201, "species_taxid": 28901, "relation_to_type": "suspected-type", "validated": true, "ani": 78.6703, "matched_fragments": 354, "total_fragments": 1582, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009738185.1", "gtdb_species": "s__Erwinia sp009738185", "ani": 100.0, "matched_fragments": 1581, "total_fragments": 1582, "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", 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"N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000026985.1", "gtdb_species": "s__Erwinia pyrifoliae", "ani": 81.52, "matched_fragments": 753, "total_fragments": 1582, "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": 81.2351, "matched_fragments": 785, "total_fragments": 1582, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.301, "doubling_h": 0.093, "growth_tmp": 28.812, "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": 0.833, "range_salinity": 1.0, "facultative_respiration": 0.666, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.333, "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", "sorbitola" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }