{ "type": "genome", "identifier": "GCF_000803215.1", "organism": "Pectobacterium fontis", "title": "Pectobacterium fontis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Malaya", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000803215.1", "bioproject": "PRJNA224116", "biosample": "SAMN03154070", "wgs_master": "JSXC00000000.1", "refseq_category": "reference genome", "taxid": "2558042", "species_taxid": "2558042", "organism_name": "Pectobacterium fontis", "infraspecific_name": "strain=M022", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/12/17", "asm_name": "ASM80321v1", "asm_submitter": "University of Malaya", "gbrs_paired_asm": "GCA_000803215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/803/215/GCF_000803215.1_ASM80321v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4151564", "genome_size_ungapped": "4151564", "gc_percent": "51.000000", "replicon_count": "0", "scaffold_count": "105", "contig_count": "105", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000803215.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3837", "protein_coding_gene_count": "3677", "non_coding_gene_count": "85", "pubmed_id": "25676763" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-12-17", "dateModified": "2014-12-17", "datePublished": "2014-12-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Pectobacterium fontis" ], "sample_taxid": [ "2558042" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Malaysia" ], "sample_host_location_id": [], "data_size": "1.185 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 28.0, "max": 28.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4151564", "Number of Sequences": "105", "Longest Sequences (bp)": "238213", "N50 (bp)": "126203", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "51.2", "Number of CDSs": "3693", "Average Protein Length": "319.2", "Coding Ratio (%)": "85.2", "Number of rRNAs": "3", "Number of tRNAs": "68", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pectobacterium fontis", "strain": "strain=M022", "accession": "GCA_000803215.1", "taxid": 2558042, "species_taxid": 2558042, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1336, "total_fragments": 1337, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium carotovorum subsp. carotovorum", "strain": "strain=NCPPB 312", "accession": "GCA_000749855.1", "taxid": 555, "species_taxid": 554, "relation_to_type": "suspected-type", "validated": true, "ani": 88.5967, "matched_fragments": 1119, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium carotovorum", "strain": "strain=DSM 30168", "accession": "GCA_900129615.1", "taxid": 554, "species_taxid": 554, "relation_to_type": "type", "validated": true, "ani": 88.5784, "matched_fragments": 1124, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium carotovorum subsp. carotovorum", "strain": "strain=ICMP 5702", "accession": "GCA_001039055.1", "taxid": 555, "species_taxid": 554, "relation_to_type": "suspected-type", "validated": true, "ani": 88.5666, "matched_fragments": 1122, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium polaris", "strain": "strain=NIBIO1006", "accession": "GCA_002307355.1", "taxid": 2042057, "species_taxid": 2042057, "relation_to_type": "type", "validated": true, "ani": 88.465, "matched_fragments": 1107, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium odoriferum", "strain": "strain=NCPPB 3839", "accession": "GCA_000754765.1", "taxid": 78398, "species_taxid": 78398, "relation_to_type": "type", "validated": true, "ani": 88.4172, "matched_fragments": 1094, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium actinidiae", "strain": "strain=KKH3", "accession": "GCA_000803315.1", "taxid": 1507808, "species_taxid": 1507808, "relation_to_type": "type", "validated": true, "ani": 88.3746, "matched_fragments": 1128, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium colocasium", "strain": "strain=LJ1", "accession": "GCA_020181655.1", "taxid": 2878098, "species_taxid": 2878098, "relation_to_type": "type", "validated": true, "ani": 88.3332, "matched_fragments": 1101, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium aquaticum", "strain": "strain=A212-S19-A16", "accession": "GCA_003382565.3", "taxid": 2204145, "species_taxid": 2204145, "relation_to_type": "type", "validated": true, "ani": 88.2568, "matched_fragments": 1052, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium brasiliense", "strain": "strain=IPO:3540 CFBP:6617 ATCC:BAA-417 IBSBF:1692", "accession": "GCA_016950255.1", "taxid": 180957, "species_taxid": 180957, "relation_to_type": "type", "validated": true, "ani": 88.2352, "matched_fragments": 1096, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium brasiliense", "strain": "strain=LMG 21371", "accession": "GCA_000754695.1", "taxid": 180957, "species_taxid": 180957, "relation_to_type": "type", "validated": true, "ani": 88.1777, "matched_fragments": 1103, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium quasiaquaticum", "strain": "strain=A477-S1-J17", "accession": "GCA_014946775.2", "taxid": 2774015, "species_taxid": 2774015, "relation_to_type": "type", "validated": true, "ani": 88.172, "matched_fragments": 1066, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium polonicum", "strain": "strain=DPMP315", "accession": "GCA_005497185.1", "taxid": 2485124, "species_taxid": 2485124, "relation_to_type": "type", "validated": true, "ani": 87.6339, "matched_fragments": 1103, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium zantedeschiae", "strain": "strain=9M", "accession": "GCA_004137795.1", "taxid": 2034769, "species_taxid": 2034769, "relation_to_type": "type", "validated": true, "ani": 87.428, "matched_fragments": 1143, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium punjabense", "strain": "strain=SS95", "accession": "GCA_003028395.1", "taxid": 2108399, "species_taxid": 2108399, "relation_to_type": "type", "validated": true, "ani": 87.1296, "matched_fragments": 1071, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia bockelmannii", "strain": "strain=S3", "accession": "GCA_008011855.1", "taxid": 2703793, "species_taxid": 2703793, "relation_to_type": "type", "validated": true, "ani": 78.7611, "matched_fragments": 388, "total_fragments": 1337, "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": 78.5964, "matched_fragments": 399, "total_fragments": 1337, "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": 78.59, "matched_fragments": 382, "total_fragments": 1337, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000803215.1", "gtdb_species": "s__Pectobacterium fontis", "ani": 100.0, "matched_fragments": 1336, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "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_900129615.1", "gtdb_species": "s__Pectobacterium carotovorum", "ani": 88.5568, "matched_fragments": 1126, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.11", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 81, "status": "-" }, { "accession": "GCF_002307355.1", "gtdb_species": "s__Pectobacterium polaris", "ani": 88.4689, "matched_fragments": 1107, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_000803315.1", "gtdb_species": "s__Pectobacterium actinidiae", "ani": 88.3746, "matched_fragments": 1128, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003382565.2", "gtdb_species": "s__Pectobacterium aquaticum", "ani": 88.2382, "matched_fragments": 1035, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.07", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_000754695.1", "gtdb_species": "s__Pectobacterium brasiliense", "ani": 88.1602, "matched_fragments": 1105, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.37", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 92, "status": "-" }, { "accession": "GCF_015689195.1", "gtdb_species": "s__Pectobacterium aroidearum", "ani": 88.14, "matched_fragments": 1116, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_013449685.1", "gtdb_species": "s__Pectobacterium brasiliense_A", "ani": 88.0301, "matched_fragments": 1068, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "96.08", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_013449375.1", "gtdb_species": "s__Pectobacterium sp013449375", "ani": 87.9454, "matched_fragments": 1072, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "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_005497185.1", "gtdb_species": "s__Pectobacterium polonicum", "ani": 87.6339, "matched_fragments": 1103, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "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_004137795.1", "gtdb_species": "s__Pectobacterium zantedeschiae", "ani": 87.4388, "matched_fragments": 1141, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_012427845.1", "gtdb_species": "s__Pectobacterium punjabense", "ani": 87.2205, "matched_fragments": 1078, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.67", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001742145.1", "gtdb_species": "s__Pectobacterium parmentieri", "ani": 87.1947, "matched_fragments": 1118, "total_fragments": 1337, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "98.87", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 33, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.104, "growth_tmp": 27.416, "optimum_tmp": 29.406, "optimum_ph": 6.25, "genome_size": 4916069.627, "gc_content": 50.885, "coding_genes": 4336.072, "rRNA16S_genes": 7.0, "tRNA_genes": 76.833, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.714, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.285, "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": [ "Pectobacterium", "fontis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }