{ "type": "genome", "identifier": "GCF_009707705.1", "organism": "Paludibacterium denitrificans", "title": "Paludibacterium denitrificans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hankyong National University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009707705.1", "bioproject": "PRJNA224116", "biosample": "SAMN13294206", "wgs_master": "WLYX00000000.1", "refseq_category": "reference genome", "taxid": "2675226", "species_taxid": "2675226", "organism_name": "Paludibacterium denitrificans", "infraspecific_name": "strain=dN18-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/11/24", "asm_name": "ASM970770v1", "asm_submitter": "Hankyong National University", "gbrs_paired_asm": "GCA_009707705.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/707/705/GCF_009707705.1_ASM970770v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3347996", "genome_size_ungapped": "3347996", "gc_percent": "57.500000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009707705.1-RS_2024_09_29", "annotation_date": "2024-09-29", "total_gene_count": "4636", "protein_coding_gene_count": "3634", "non_coding_gene_count": "114", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-11-24", "dateModified": "2019-11-24", "datePublished": "2019-11-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Paludibacterium denitrificans" ], "sample_taxid": [ "2675226" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Suwon" ], "sample_host_location_id": [], "data_size": "0.943 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.2, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3347996", "Number of Sequences": "3", "Longest Sequences (bp)": "3165109", "N50 (bp)": "3165109", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.3", "Number of CDSs": "5172", "Average Protein Length": "178.0", "Coding Ratio (%)": "82.5", "Number of rRNAs": "22", "Number of tRNAs": "85", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Aquitalea aquatilis", "strain": "strain=THG-DN7.12", "accession": "GCA_005155025.1", "taxid": 1537400, "species_taxid": 1537400, "relation_to_type": "type", "validated": true, "ani": 80.2105, "matched_fragments": 517, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquitalea denitrificans", "strain": "strain=5YN1-3", "accession": "GCA_009856625.1", "taxid": 519081, "species_taxid": 519081, "relation_to_type": "type", "validated": true, "ani": 80.1419, "matched_fragments": 487, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquitalea magnusonii", "strain": "strain=DSM 25134", "accession": "GCA_003202035.1", "taxid": 332411, "species_taxid": 332411, "relation_to_type": "suspected-type", "validated": true, "ani": 79.9409, "matched_fragments": 499, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquitalea pelogenes", "strain": "strain=CCM 7557", "accession": "GCA_001515305.1", "taxid": 1293573, "species_taxid": 1293573, "relation_to_type": "type", "validated": true, "ani": 79.777, "matched_fragments": 466, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium sphagni", "strain": "strain=IIBBL 14B-1", "accession": "GCA_001855555.1", "taxid": 1903179, "species_taxid": 1903179, "relation_to_type": "type", "validated": true, "ani": 79.3391, "matched_fragments": 384, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium violaceum", "strain": "strain=ATCC 12472", "accession": "GCA_000007705.1", "taxid": 536, "species_taxid": 536, "relation_to_type": "type", "validated": true, "ani": 79.2599, "matched_fragments": 403, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium amazonense", "strain": "strain=DSM 26508", "accession": "GCA_001855565.1", "taxid": 1382803, "species_taxid": 1382803, "relation_to_type": "type", "validated": true, "ani": 79.2041, "matched_fragments": 381, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium paludis", "strain": "strain=IIBBL 257-1", "accession": "GCA_008275125.1", "taxid": 2605945, "species_taxid": 2605945, "relation_to_type": "type", "validated": true, "ani": 79.1393, "matched_fragments": 413, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium phragmitis", "strain": "strain=IIBBL 112-1", "accession": "GCA_003325475.1", "taxid": 2202141, "species_taxid": 2202141, "relation_to_type": "type", "validated": true, "ani": 79.137, "matched_fragments": 385, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium violaceum", "strain": "strain=NCTC9757", "accession": "GCA_900446805.1", "taxid": 536, "species_taxid": 536, "relation_to_type": "type", "validated": true, "ani": 79.1026, "matched_fragments": 409, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium aquaticum", "strain": "strain=DSM 19852", "accession": "GCA_021129195.1", "taxid": 467180, "species_taxid": 467180, "relation_to_type": "type", "validated": true, "ani": 79.0677, "matched_fragments": 391, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium sinusclupearum", "strain": "strain=MWU13-2610", "accession": "GCA_002902845.1", "taxid": 2077146, "species_taxid": 2077146, "relation_to_type": "type", "validated": true, "ani": 79.0008, "matched_fragments": 375, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium alkanivorans", "strain": "strain=IITR-71", "accession": "GCA_016937655.1", "taxid": 1071719, "species_taxid": 1071719, "relation_to_type": "type", "validated": true, "ani": 78.964, "matched_fragments": 417, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vogesella urethralis", "strain": "strain=YM-1", "accession": "GCA_007644045.2", "taxid": 2592656, "species_taxid": 2592656, "relation_to_type": "type", "validated": true, "ani": 78.9436, "matched_fragments": 387, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium alticapitis", "strain": "strain=MWU14-2602", "accession": "GCA_002924365.1", "taxid": 2073169, "species_taxid": 2073169, "relation_to_type": "type", "validated": true, "ani": 78.8852, "matched_fragments": 352, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium vaccinii", "strain": "strain=MWU205", "accession": "GCA_000971335.1", "taxid": 1108595, "species_taxid": 1108595, "relation_to_type": "type", "validated": true, "ani": 78.8352, "matched_fragments": 378, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vogesella mureinivorans", "strain": "strain=389", "accession": "GCA_007644035.2", "taxid": 657276, "species_taxid": 657276, "relation_to_type": "type", "validated": true, "ani": 78.6595, "matched_fragments": 346, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromobacterium piscinae", "strain": "strain=DSM 23278", "accession": "GCA_021129175.1", "taxid": 686831, "species_taxid": 686831, "relation_to_type": "type", "validated": true, "ani": 78.624, "matched_fragments": 378, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rivicola pingtungensis", "strain": "strain=DSM 29661", "accession": "GCA_003201855.1", "taxid": 1054498, "species_taxid": 1054498, "relation_to_type": "type", "validated": true, "ani": 78.2178, "matched_fragments": 252, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gulbenkiania indica", "strain": "strain=DSM 17901", "accession": "GCA_001517245.1", "taxid": 375574, "species_taxid": 375574, "relation_to_type": "type", "validated": true, "ani": 78.0547, "matched_fragments": 301, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gulbenkiania indica", "strain": "strain=DSM 17901", "accession": "GCA_001418035.1", "taxid": 375574, "species_taxid": 375574, "relation_to_type": "type", "validated": true, "ani": 78.0547, "matched_fragments": 301, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquaspirillum serpens", "strain": "strain=DSM 68", "accession": "GCA_000420525.1", "taxid": 190, "species_taxid": 190, "relation_to_type": "type", "validated": true, "ani": 76.7857, "matched_fragments": 59, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidimonas thermarum", "strain": "strain=AA-1", "accession": "GCA_007556705.1", "taxid": 335431, "species_taxid": 335431, "relation_to_type": "type", "validated": true, "ani": 76.504, "matched_fragments": 67, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Aquabacterium soli", "strain": "strain=SJQ9", "accession": "GCA_003933735.1", "taxid": 2493092, "species_taxid": 2493092, "relation_to_type": "type", "validated": true, "ani": 76.3617, "matched_fragments": 72, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinibacter tainanensis", "strain": "strain=DSM 15459", "accession": "GCA_000429785.1", "taxid": 230667, "species_taxid": 230667, "relation_to_type": "type", "validated": true, "ani": 76.129, "matched_fragments": 92, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax caeni", "strain": "strain=R-24608", "accession": "GCA_900116825.1", "taxid": 343013, "species_taxid": 343013, "relation_to_type": "type", "validated": true, "ani": 75.9456, "matched_fragments": 62, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Comamonas avium", "strain": "strain=Sa2CVA6", "accession": "GCA_014836675.1", "taxid": 2762231, "species_taxid": 2762231, "relation_to_type": "type", "validated": true, "ani": 75.9259, "matched_fragments": 50, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Comamonas koreensis", "strain": "strain=KCTC 12005", "accession": "GCA_021026195.1", "taxid": 160825, "species_taxid": 160825, "relation_to_type": "type", "validated": true, "ani": 75.6827, "matched_fragments": 76, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax konjaci", "strain": "strain=DSM 7481", "accession": "GCA_900112675.1", "taxid": 32040, "species_taxid": 32040, "relation_to_type": "type", "validated": true, "ani": 75.4258, "matched_fragments": 59, "total_fragments": 1115, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.2, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_009707705.1", "gtdb_species": "s__WLYX01 sp009707705", "ani": 100.0, "matched_fragments": 1114, "total_fragments": 1115, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__WLYX01", "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_005155025.1", "gtdb_species": "s__Aquitalea aquatilis", "ani": 80.2182, "matched_fragments": 513, "total_fragments": 1115, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.19", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", 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"status": "-" }, { "accession": "GCF_003693445.1", "gtdb_species": "s__Aquitalea sp003693445", "ani": 79.9318, "matched_fragments": 480, "total_fragments": 1115, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea", "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_003202035.1", "gtdb_species": "s__Aquitalea magnusonii", "ani": 79.9299, "matched_fragments": 500, "total_fragments": 1115, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": 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"s__Chromobacterium violaceum", "ani": 79.1732, "matched_fragments": 399, "total_fragments": 1115, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "98.16", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_900090205.1", "gtdb_species": "s__Vogesella sp900090205", "ani": 79.1658, "matched_fragments": 392, "total_fragments": 1115, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella", "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_003325475.1", "gtdb_species": "s__Chromobacterium 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