{ "type": "genome", "identifier": "GCF_013307225.1", "organism": "Polynucleobacter tropicus", "title": "Polynucleobacter tropicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Innsbruck", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013307225.1", "bioproject": "PRJNA224116", "biosample": "SAMN08941742", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1743174", "species_taxid": "1743174", "organism_name": "Polynucleobacter tropicus", "infraspecific_name": "strain=MWH-UH21B", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/09", "asm_name": "ASM1330722v1", "asm_submitter": "University of Innsbruck", "gbrs_paired_asm": "GCA_013307225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/307/225/GCF_013307225.1_ASM1330722v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2040807", "genome_size_ungapped": "2040807", "gc_percent": "45.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013307225.1-RS_2024_07_23", "annotation_date": "2024-07-23", "total_gene_count": "2092", "protein_coding_gene_count": "2035", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-09", "dateModified": "2020-06-09", "datePublished": "2020-06-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Polynucleobacter tropicus" ], "sample_taxid": [ "1743174" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Uganda: Kagona wetland, Nabugabo, Masaka" ], "sample_host_location_id": [], "data_size": "0.581 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)": "2040807", "Number of Sequences": "1", "Longest Sequences (bp)": "2040807", "N50 (bp)": "2040807", "Gap Ratio (%)": "0.000441", "GCcontent (%)": "45.1", "Number of CDSs": "2011", "Average Protein Length": "311.7", "Coding Ratio (%)": "92.2", "Number of rRNAs": "3", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Polynucleobacter tropicus", "strain": "strain=MWH-UH21B", "accession": "GCA_013307225.1", "taxid": 1743174, "species_taxid": 1743174, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 680, "total_fragments": 680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Polynucleobacter parvulilacunae", "strain": "strain=Ross1-W9", "accession": "GCA_018881715.1", "taxid": 1855631, "species_taxid": 1855631, "relation_to_type": "type", "validated": true, "ani": 80.8902, "matched_fragments": 340, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter yangtzensis", "strain": "strain=MWH-JaK3", "accession": "GCA_001595965.1", "taxid": 1743159, "species_taxid": 1743159, "relation_to_type": "type", "validated": true, "ani": 80.6078, "matched_fragments": 358, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter wuianus", "strain": "strain=QLW-P1FAT50C-4", "accession": "GCA_001659725.1", "taxid": 1743168, "species_taxid": 1743168, "relation_to_type": "type", "validated": true, "ani": 80.5442, "matched_fragments": 411, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter hirudinilacicola", "strain": "strain=MWH-EgelM1-30-B4", "accession": "GCA_002192535.1", "taxid": 1743166, "species_taxid": 1743166, "relation_to_type": "type", "validated": true, "ani": 80.4562, "matched_fragments": 325, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter ibericus", "strain": "strain=es-MAR-2", "accession": "GCA_018687955.1", "taxid": 1819725, "species_taxid": 1819725, "relation_to_type": "type", "validated": true, "ani": 80.3962, "matched_fragments": 325, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter asymbioticus", "strain": "strain=QLW-P1DMWA-1", "accession": "GCA_000016345.1", "taxid": 576611, "species_taxid": 576611, "relation_to_type": "type", "validated": true, "ani": 80.0697, "matched_fragments": 338, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter nymphae", "strain": "strain=AP-Mumm-500A-B3", "accession": "GCA_018882155.1", "taxid": 2081043, "species_taxid": 2081043, "relation_to_type": "type", "validated": true, "ani": 79.8454, "matched_fragments": 316, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter alcilacus", "strain": "strain=UK-Pondora-W15", "accession": "GCA_018881545.1", "taxid": 1819739, "species_taxid": 1819739, "relation_to_type": "type", "validated": true, "ani": 79.595, "matched_fragments": 295, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter finlandensis", "strain": "strain=MWH-Mekk-B1", "accession": "GCA_018881755.1", "taxid": 1855894, "species_taxid": 1855894, "relation_to_type": "type", "validated": true, "ani": 79.359, "matched_fragments": 300, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter paneuropaeus", "strain": "strain=MG-25-Pas1-D2", "accession": "GCA_003261235.1", "taxid": 2527775, "species_taxid": 2527775, "relation_to_type": "type", "validated": true, "ani": 79.2387, "matched_fragments": 195, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013307225.1", "gtdb_species": "s__Polynucleobacter sp013307225", "ani": 100.0, "matched_fragments": 680, "total_fragments": 680, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter", "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_018687095.1", "gtdb_species": "s__Polynucleobacter sp018687095", "ani": 88.3586, "matched_fragments": 517, "total_fragments": 680, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter", "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_018687195.1", "gtdb_species": "s__Polynucleobacter sp018687195", "ani": 85.0438, "matched_fragments": 537, "total_fragments": 680, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter", "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_018881575.1", "gtdb_species": "s__Polynucleobacter sp018881575", "ani": 80.959, "matched_fragments": 353, "total_fragments": 680, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter", "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_018687455.1", "gtdb_species": "s__Polynucleobacter sp001870365", "ani": 80.7432, "matched_fragments": 363, "total_fragments": 680, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.21", "min_intra_species_ani": "96.15", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018688095.1", "gtdb_species": 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