{ "type": "genome", "identifier": "GCF_004342425.1", "organism": "Dokdonella fugitiva", "title": "Dokdonella fugitiva", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004342425.1", "bioproject": "PRJNA224116", "biosample": "SAMN10864717", "wgs_master": "SLWQ00000000.1", "refseq_category": "reference genome", "taxid": "328517", "species_taxid": "328517", "organism_name": "Dokdonella fugitiva", "infraspecific_name": "strain=A3", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/11", "asm_name": "ASM434242v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004342425.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/342/425/GCF_004342425.1_ASM434242v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4280142", "genome_size_ungapped": "4279357", "gc_percent": "69.500000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004342425.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "3684", "protein_coding_gene_count": "3588", "non_coding_gene_count": "52", "pubmed_id": "26203337" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-11", "dateModified": "2019-03-11", "datePublished": "2019-03-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Dokdonella fugitiva" ], "sample_taxid": [ "328517" ], "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": "1.139 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)": "4280142", "Number of Sequences": "35", "Longest Sequences (bp)": "996640", "N50 (bp)": "296365", "Gap Ratio (%)": "0.018341", "GCcontent (%)": "69.4", "Number of CDSs": "3629", "Average Protein Length": "350.0", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Dokdonella fugitiva", "strain": "strain=A3", "accession": "GCA_004342425.1", "taxid": 328517, "species_taxid": 328517, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1407, "total_fragments": 1408, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Dokdonella koreensis", "strain": "strain=DS-123", "accession": "GCA_001632775.1", "taxid": 323415, "species_taxid": 323415, "relation_to_type": "type", "validated": true, "ani": 79.6716, "matched_fragments": 654, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tahibacter caeni", "strain": "strain=BUT-6", "accession": "GCA_024609805.1", "taxid": 1453545, "species_taxid": 1453545, "relation_to_type": "type", "validated": true, "ani": 79.5826, "matched_fragments": 640, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rudaea cellulosilytica", "strain": "strain=DSM 22992", "accession": "GCA_000378125.1", "taxid": 540746, "species_taxid": 540746, "relation_to_type": "type", "validated": true, "ani": 79.0767, "matched_fragments": 552, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=DSM 14263", "accession": "GCA_003148905.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 79.0108, "matched_fragments": 561, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=LMG 19981", "accession": "GCA_006352285.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 78.9639, "matched_fragments": 537, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dokdonella immobilis", "strain": "strain=CGMCC 1.7659", "accession": "GCA_900115085.1", "taxid": 578942, "species_taxid": 578942, "relation_to_type": "type", "validated": true, "ani": 78.7586, "matched_fragments": 519, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodanobacter thiooxydans", "strain": "strain=LCS2", "accession": "GCA_000264375.1", "taxid": 416169, "species_taxid": 416169, "relation_to_type": "type", "validated": true, "ani": 78.7512, "matched_fragments": 449, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vulcaniibacterium thermophilum", "strain": "strain=KCTC 32020", "accession": "GCA_014656335.1", "taxid": 1169913, "species_taxid": 1169913, "relation_to_type": "type", "validated": true, "ani": 78.5727, "matched_fragments": 490, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Frateuria flava", "strain": "strain=MAH-13", "accession": "GCA_017837635.1", "taxid": 2821489, "species_taxid": 2821489, "relation_to_type": "type", "validated": true, "ani": 78.5038, "matched_fragments": 455, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella solisilvae", "strain": "strain=DHG54", "accession": "GCA_003351225.1", "taxid": 1920168, "species_taxid": 1920168, "relation_to_type": "type", "validated": true, "ani": 78.2714, "matched_fragments": 414, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteibacter yeojuensis", "strain": "strain=DSM 17673", "accession": "GCA_011742875.1", "taxid": 345309, "species_taxid": 345309, "relation_to_type": "type", "validated": true, "ani": 78.1689, "matched_fragments": 389, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas taiwanensis", "strain": "strain=DSM 22914", "accession": "GCA_010093135.1", "taxid": 176598, "species_taxid": 176598, "relation_to_type": "type", "validated": true, "ani": 78.0566, "matched_fragments": 369, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella telluris", "strain": "strain=G9", "accession": "GCA_014297575.1", "taxid": 2763498, "species_taxid": 2763498, "relation_to_type": "type", "validated": true, "ani": 77.9841, "matched_fragments": 367, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella japonica", "strain": "strain=DSM 16301", "accession": "GCA_001010355.1", "taxid": 231455, "species_taxid": 231455, "relation_to_type": "type", "validated": true, "ani": 77.9181, "matched_fragments": 310, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella acidiphila", "strain": "strain=7MK23", "accession": "GCA_014863405.1", "taxid": 2775866, "species_taxid": 2775866, "relation_to_type": "type", "validated": true, "ani": 77.7344, "matched_fragments": 337, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tahibacter aquaticus", "strain": "strain=DSM 21667", "accession": "GCA_004363655.1", "taxid": 520092, "species_taxid": 520092, "relation_to_type": "type", "validated": true, "ani": 77.6408, "matched_fragments": 535, "total_fragments": 1408, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004342425.1", "gtdb_species": "s__Dokdonella_A fugitiva", "ani": 100.0, "matched_fragments": 1407, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "99.45", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014138265.1", "gtdb_species": "s__Dokdonella_A fugitiva_A", "ani": 88.9309, "matched_fragments": 1177, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "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": "GCA_009996615.1", "gtdb_species": "s__Dokdonella_A sp009996615", "ani": 83.1583, "matched_fragments": 828, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "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": "GCA_017744955.1", "gtdb_species": "s__Dokdonella_A sp017744955", "ani": 82.4084, "matched_fragments": 900, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "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": "GCA_002297645.1", "gtdb_species": "s__Dokdonella_A sp002297645", "ani": 82.239, "matched_fragments": 683, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.81", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_004143945.1", "gtdb_species": "s__Dokdonella_A sp004143945", "ani": 82.2365, "matched_fragments": 832, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "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": "GCA_014338185.1", "gtdb_species": "s__Dokdonella_A sp014338185", "ani": 81.0246, "matched_fragments": 636, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.24", "min_intra_species_ani": "96.24", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003241385.1", "gtdb_species": "s__Dokdonella denitrificans_A", "ani": 80.0261, "matched_fragments": 688, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella", "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_003148905.1", "gtdb_species": "s__Fulvimonas soli", "ani": 78.9936, "matched_fragments": 563, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900112865.1", "gtdb_species": "s__Dyella marensis", "ani": 78.4794, "matched_fragments": 523, "total_fragments": 1408, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.09, "cell_length": 0.357, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 29.0, "optimum_ph": 6.7, "genome_size": 4541227.166, "gc_content": 70.3, "coding_genes": 3647.0, "rRNA16S_genes": 2.0, "tRNA_genes": 47.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.2, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "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": [ "Dokdonella", "fugitiva" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }