{ "type": "genome", "identifier": "GCF_000749905.1", "organism": "Pectobacterium atrosepticum", "title": "Pectobacterium atrosepticum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Food and Environment Research Agency", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000749905.1", "bioproject": "PRJNA224116", "biosample": "SAMN02999423", "wgs_master": "JQHK00000000.1", "refseq_category": "na", "taxid": "29471", "species_taxid": "29471", "organism_name": "Pectobacterium atrosepticum", "infraspecific_name": "strain=NCPPB 549", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/09/08", "asm_name": "ASM74990v1", "asm_submitter": "Food and Environment Research Agency", "gbrs_paired_asm": "GCA_000749905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/749/905/GCF_000749905.1_ASM74990v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5104595", "genome_size_ungapped": "5104595", "gc_percent": "51.000000", "replicon_count": "0", "scaffold_count": "60", "contig_count": "60", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000749905.1-RS_2024_05_16", "annotation_date": "2024-05-16", "total_gene_count": "4639", "protein_coding_gene_count": "4465", "non_coding_gene_count": "90", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-09-08", "dateModified": "2014-09-08", "datePublished": "2014-09-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Pectobacterium atrosepticum" ], "sample_taxid": [ "29471" ], "sample_host_organism": [ "Solanum tuberosum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "1.453 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)": "5104595", "Number of Sequences": "60", "Longest Sequences (bp)": "559098", "N50 (bp)": "395607", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.9", "Number of CDSs": "4519", "Average Protein Length": "319.0", "Coding Ratio (%)": "84.7", "Number of rRNAs": "3", "Number of tRNAs": "71", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pectobacterium atrosepticum", "strain": "strain=NCPPB 549", "accession": "GCA_000749905.1", "taxid": 29471, "species_taxid": 29471, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1679, "total_fragments": 1682, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium atrosepticum", "strain": "strain=ICMP 1526", "accession": "GCA_001038685.1", "taxid": 29471, "species_taxid": 29471, "relation_to_type": "type", "validated": true, "ani": 99.9851, "matched_fragments": 1596, "total_fragments": 1682, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pectobacterium peruviense", "strain": "strain=IFB5232", "accession": "GCA_002847345.1", "taxid": 2066479, "species_taxid": 2066479, "relation_to_type": "type", "validated": true, "ani": 93.8672, "matched_fragments": 1425, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium betavasculorum", "strain": "strain=NCPPB 2795", "accession": "GCA_000749845.1", "taxid": 55207, "species_taxid": 55207, "relation_to_type": "type", "validated": true, "ani": 92.0817, "matched_fragments": 1271, "total_fragments": 1682, "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": 91.3207, "matched_fragments": 1358, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium wasabiae", "strain": "strain=CFBP 3304", "accession": "GCA_000291725.1", "taxid": 55208, "species_taxid": 55208, "relation_to_type": "type", "validated": true, "ani": 89.9815, "matched_fragments": 1277, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium wasabiae", "strain": "strain=CFBP 3304", "accession": "GCA_001742185.1", "taxid": 55208, "species_taxid": 55208, "relation_to_type": "type", "validated": true, "ani": 89.9788, "matched_fragments": 1297, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium parvum", "strain": "strain=s0421", "accession": "GCA_900195285.2", "taxid": 2778550, "species_taxid": 2778550, "relation_to_type": "type", "validated": true, "ani": 89.83, "matched_fragments": 1234, "total_fragments": 1682, "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": 89.8289, "matched_fragments": 1336, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pectobacterium parmentieri", "strain": "strain=RNS 08-42-1A", "accession": "GCA_001742145.1", "taxid": 1905730, "species_taxid": 1905730, "relation_to_type": "type", "validated": true, "ani": 89.8149, "matched_fragments": 1298, "total_fragments": 1682, "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": 89.3217, "matched_fragments": 1201, "total_fragments": 1682, "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": 88.5507, "matched_fragments": 1292, "total_fragments": 1682, "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": 78.7086, "matched_fragments": 372, "total_fragments": 1682, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella bonaserana", "strain": "strain=H11b", "accession": "GCA_019049675.1", "taxid": 2816248, 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atrosepticum", "ani": 99.9809, "matched_fragments": 1651, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_002847345.1", "gtdb_species": "s__Pectobacterium peruviense", "ani": 93.8672, "matched_fragments": 1425, "total_fragments": 1682, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "97.64", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000749845.1", "gtdb_species": 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