{ "type": "genome", "identifier": "GCF_900187875.1", "organism": "Polynucleobacter victoriensis", "title": "Polynucleobacter victoriensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900187875.1", "bioproject": "PRJNA224116", "biosample": "SAMN06295916", "wgs_master": "FYEX00000000.1", "refseq_category": "reference genome", "taxid": "2049319", "species_taxid": "2049319", "organism_name": "Polynucleobacter victoriensis", "infraspecific_name": "strain=MWH-VicM1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/06/26", "asm_name": "IMG-taxon 2710264786 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900187875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/187/875/GCF_900187875.1_IMG-taxon_2710264786_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1626636", "genome_size_ungapped": "1626636", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900187875.1-RS_2024_04_15", "annotation_date": "2024-04-15", "total_gene_count": "1677", "protein_coding_gene_count": "1625", "non_coding_gene_count": "41", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-06-26", "dateModified": "2017-06-26", "datePublished": "2017-06-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Polynucleobacter victoriensis" ], "sample_taxid": [ "2049319" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Uganda: Kampala" ], "sample_host_location_id": [], "data_size": "0.462 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)": "1626636", "Number of Sequences": "3", "Longest Sequences (bp)": "1230501", "N50 (bp)": "1230501", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.1", "Number of CDSs": "1621", "Average Protein Length": "312.3", "Coding Ratio (%)": "93.4", "Number of rRNAs": "3", "Number of tRNAs": "35", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Polynucleobacter victoriensis", "strain": "strain=MWH-VicM1", "accession": "GCA_900187875.1", "taxid": 2049319, "species_taxid": 2049319, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 541, "total_fragments": 541, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Polynucleobacter cosmopolitanus", "strain": "strain=MWH-MoIso2", "accession": "GCA_002224225.1", "taxid": 351345, "species_taxid": 351345, "relation_to_type": "type", "validated": true, "ani": 80.452, "matched_fragments": 321, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter bastaniensis", "strain": "strain=AP-Basta-1000A-D1", "accession": "GCA_018882205.1", "taxid": 2081039, "species_taxid": 2081039, "relation_to_type": "type", "validated": true, "ani": 77.9326, "matched_fragments": 75, "total_fragments": 541, "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": 77.8739, "matched_fragments": 86, "total_fragments": 541, "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": 77.6086, "matched_fragments": 95, "total_fragments": 541, "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": 77.5569, "matched_fragments": 90, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter corsicus", "strain": "strain=AP-Melu-1000-A1", "accession": "GCA_018688255.1", "taxid": 2081042, "species_taxid": 2081042, "relation_to_type": "type", "validated": true, "ani": 77.4322, "matched_fragments": 80, "total_fragments": 541, "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": 77.3925, "matched_fragments": 91, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter parvulilacunae", "strain": "strain=Ross1-W9", "accession": "GCA_018881715.1", "taxid": 1855631, "species_taxid": 1855631, "relation_to_type": "type", "validated": true, "ani": 77.2481, "matched_fragments": 90, "total_fragments": 541, "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": 77.2234, "matched_fragments": 90, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polynucleobacter difficilis", "strain": "strain=AM-8B5", "accession": "GCA_003065365.1", "taxid": 556054, "species_taxid": 556054, "relation_to_type": "type", "validated": true, "ani": 77.1982, "matched_fragments": 56, "total_fragments": 541, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900187875.1", "gtdb_species": "s__Polynucleobacter victoriensis", "ani": 100.0, "matched_fragments": 541, "total_fragments": 541, "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_018687615.1", "gtdb_species": "s__Polynucleobacter sp018687615", "ani": 81.1443, "matched_fragments": 321, "total_fragments": 541, "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_018882285.1", "gtdb_species": "s__Polynucleobacter sp018882285", "ani": 80.9933, "matched_fragments": 313, "total_fragments": 541, "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": "GCA_008015455.1", "gtdb_species": "s__Polynucleobacter sp008015455", "ani": 80.518, "matched_fragments": 219, "total_fragments": 541, "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_002224225.1", "gtdb_species": "s__Polynucleobacter cosmopolitanus", "ani": 80.452, "matched_fragments": 321, "total_fragments": 541, "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_018882385.1", "gtdb_species": "s__Polynucleobacter sp018882385", "ani": 80.0104, "matched_fragments": 268, "total_fragments": 541, "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_018881635.1", "gtdb_species": "s__Polynucleobacter sp018881635", "ani": 77.5998, "matched_fragments": 76, "total_fragments": 541, "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_002192535.1", "gtdb_species": "s__Polynucleobacter hirudinilacicola", "ani": 77.2234, "matched_fragments": 90, "total_fragments": 541, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.45, "cell_length": -0.029, "doubling_h": null, "growth_tmp": 25.5, "optimum_tmp": 20.0, "optimum_ph": 6.2, "genome_size": 1985362.708, "gc_content": 46.363, "coding_genes": 1918.652, "rRNA16S_genes": 1.0, "tRNA_genes": 37.981, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.25, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.75, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.8, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.2, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Polynucleobacter", "victoriensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }