{ "type": "genome", "identifier": "GCF_014191875.1", "organism": "Pseudoduganella violacea", "title": "Pseudoduganella violacea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014191875.1", "bioproject": "PRJNA224116", "biosample": "SAMN12025096", "wgs_master": "JACHXD000000000.1", "refseq_category": "reference genome", "taxid": "1715466", "species_taxid": "1715466", "organism_name": "Pseudoduganella violacea", "infraspecific_name": "strain=CECT 8897", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1419187v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014191875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/191/875/GCF_014191875.1_ASM1419187v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6247076", "genome_size_ungapped": "6247076", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "49", "contig_count": "49", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014191875.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "5597", "protein_coding_gene_count": "5487", "non_coding_gene_count": "76", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoduganella violacea" ], "sample_taxid": [ "1715466" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.721 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)": "6247076", "Number of Sequences": "49", "Longest Sequences (bp)": "715303", "N50 (bp)": "289270", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.6", "Number of CDSs": "5490", "Average Protein Length": "345.1", "Coding Ratio (%)": "91.0", "Number of rRNAs": "1", "Number of tRNAs": "72", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoduganella violacea", "strain": "strain=CECT 8897", "accession": "GCA_014191875.1", "taxid": 1715466, "species_taxid": 1715466, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2055, "total_fragments": 2057, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoduganella aquatica", "strain": "strain=FT127W", "accession": "GCA_009857595.1", "taxid": 2660641, "species_taxid": 2660641, "relation_to_type": "type", "validated": true, "ani": 82.9871, "matched_fragments": 1173, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella namucuonensis", "strain": "strain=CGMCC 1.11014", "accession": "GCA_900116645.1", "taxid": 1035707, "species_taxid": 1035707, "relation_to_type": "type", "validated": true, "ani": 82.6523, "matched_fragments": 1181, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rugamonas brunnea", "strain": "strain=LX20W", "accession": "GCA_014042345.1", "taxid": 2758569, "species_taxid": 2758569, "relation_to_type": "type", "validated": true, "ani": 82.4373, "matched_fragments": 1047, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rugamonas fusca", "strain": "strain=FT3S", "accession": "GCA_014042365.1", "taxid": 2758568, "species_taxid": 2758568, "relation_to_type": "type", "validated": true, "ani": 82.3277, "matched_fragments": 1040, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rugamonas apoptosis", "strain": "strain=LX47W", "accession": "GCA_014042355.1", "taxid": 2758570, "species_taxid": 2758570, "relation_to_type": "type", "validated": true, "ani": 82.2416, "matched_fragments": 1037, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella alba", "strain": "strain=FT9W", "accession": "GCA_009674495.1", "taxid": 2666081, "species_taxid": 2666081, "relation_to_type": "type", "validated": true, "ani": 82.1782, "matched_fragments": 1063, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella aquatilis", "strain": "strain=FT26W", "accession": "GCA_009674565.1", "taxid": 2666082, "species_taxid": 2666082, "relation_to_type": "type", "validated": true, "ani": 82.0986, "matched_fragments": 1075, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella aceris", "strain": "strain=SAP-35", "accession": "GCA_011090165.1", "taxid": 2703883, "species_taxid": 2703883, "relation_to_type": "type", "validated": true, "ani": 82.0384, "matched_fragments": 1079, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella buxea", "strain": "strain=KCTC 52429", "accession": "GCA_009720835.1", "taxid": 1949069, "species_taxid": 1949069, "relation_to_type": "type", "validated": true, "ani": 82.035, "matched_fragments": 1044, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella buxea", "strain": "strain=CGMCC 1.15931", "accession": "GCA_014644155.1", "taxid": 1949069, "species_taxid": 1949069, "relation_to_type": "type", "validated": true, "ani": 81.9944, "matched_fragments": 1067, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella armeniaca", "strain": "strain=ZMN-3", "accession": "GCA_003028855.1", "taxid": 2072590, "species_taxid": 2072590, "relation_to_type": "type", "validated": true, "ani": 81.9047, "matched_fragments": 1112, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella plicata", "strain": "strain=DSM 17505", "accession": "GCA_004421005.1", "taxid": 321984, "species_taxid": 321984, "relation_to_type": "type", "validated": true, "ani": 81.1953, "matched_fragments": 1003, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Duganella phyllosphaerae", "strain": "strain=T54", "accession": "GCA_001758785.1", "taxid": 762836, "species_taxid": 762836, "relation_to_type": "type", "validated": true, "ani": 81.0965, "matched_fragments": 923, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoduganella rivuli", "strain": "strain=FT92W", "accession": "GCA_009674485.1", "taxid": 2666085, "species_taxid": 2666085, "relation_to_type": "type", "validated": true, "ani": 80.9718, "matched_fragments": 1024, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia cavernae", "strain": "strain=K1S02-61", "accession": "GCA_003590855.1", "taxid": 2320864, "species_taxid": 2320864, "relation_to_type": "type", "validated": true, "ani": 80.9206, "matched_fragments": 759, "total_fragments": 2057, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014191875.1", "gtdb_species": "s__Pseudoduganella violacea", "ani": 100.0, "matched_fragments": 2055, "total_fragments": 2057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_001191005.1", "gtdb_species": "s__Pseudoduganella sp001191005", "ani": 93.7106, "matched_fragments": 1832, "total_fragments": 2057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_013369485.1", "gtdb_species": "s__Pseudoduganella sp013369485", "ani": 93.4044, 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"matched_fragments": 1229, "total_fragments": 2057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_001425045.1", "gtdb_species": "s__Pseudoduganella sp001425045", "ani": 82.6972, "matched_fragments": 1238, "total_fragments": 2057, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella", "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_900116645.1", "gtdb_species": "s__Pseudoduganella namucuonensis", "ani": 82.6358, 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudoduganella", "violacea" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }