{ "type": "genome", "identifier": "GCF_900454465.1", "organism": "Pannonibacter phragmitetus", "title": "Pannonibacter phragmitetus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900454465.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4412710", "wgs_master": "UGSK00000000.1", "refseq_category": "reference genome", "taxid": "121719", "species_taxid": "121719", "organism_name": "Pannonibacter phragmitetus", "infraspecific_name": "strain=NCTC13350", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "50766_H01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900454465.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/454/465/GCF_900454465.1_50766_H01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4837487", "genome_size_ungapped": "4837487", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900454465.1-RS_2024_04_25", "annotation_date": "2024-04-25", "total_gene_count": "4304", "protein_coding_gene_count": "4209", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Pannonibacter phragmitetus" ], "sample_taxid": [ "121719" ], "sample_host_organism": [ "environmental" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.336 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)": "4837487", "Number of Sequences": "2", "Longest Sequences (bp)": "4621478", "N50 (bp)": "4621478", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.1", "Number of CDSs": "4287", "Average Protein Length": "329.7", "Coding Ratio (%)": "87.7", "Number of rRNAs": "9", "Number of tRNAs": "55", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pannonibacter phragmitetus", "strain": "strain=NCTC13350", "accession": "GCA_900454465.1", "taxid": 121719, "species_taxid": 121719, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1612, "total_fragments": 1612, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pannonibacter phragmitetus", "strain": "strain=DSM 14782", "accession": "GCA_000382365.1", "taxid": 121719, "species_taxid": 121719, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9715, "matched_fragments": 1569, "total_fragments": 1612, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001517385.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 93.5121, "matched_fragments": 1277, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001418225.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 93.5121, "matched_fragments": 1277, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter carbonis", "strain": "strain=Q4.6", "accession": "GCA_003012935.1", "taxid": 2067569, "species_taxid": 2067569, "relation_to_type": "type", "validated": true, "ani": 81.0619, "matched_fragments": 804, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium suaedae", "strain": "strain=DSM 22153", "accession": "GCA_900142725.1", "taxid": 735517, "species_taxid": 735517, "relation_to_type": "type", "validated": true, "ani": 79.2421, "matched_fragments": 580, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stappia albiluteola", "strain": "strain=F7233", "accession": "GCA_014050225.1", "taxid": 2758565, "species_taxid": 2758565, "relation_to_type": "type", "validated": true, "ani": 78.67, "matched_fragments": 437, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 77.8793, "matched_fragments": 336, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella sumterensis", "strain": "strain=MEC087", "accession": "GCA_004514425.2", "taxid": 1967501, "species_taxid": 1967501, "relation_to_type": "type", "validated": true, "ani": 77.7013, "matched_fragments": 313, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter oligotrophicus", "strain": "strain=29k", "accession": "GCA_008364685.1", "taxid": 2607286, "species_taxid": 2607286, "relation_to_type": "type", "validated": true, "ani": 77.2377, "matched_fragments": 288, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoligotrophos defluvii", "strain": "strain=lm1", "accession": "GCA_005281615.1", "taxid": 2561934, "species_taxid": 2561934, "relation_to_type": "type", "validated": true, "ani": 76.3981, "matched_fragments": 182, "total_fragments": 1612, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000382365.1", "gtdb_species": "s__Pannonibacter phragmitetus", "ani": 99.9715, "matched_fragments": 1569, "total_fragments": 1612, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter", "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": "conclusive" }, { "accession": "GCF_001418225.1", "gtdb_species": "s__Pannonibacter indicus", "ani": 93.5121, "matched_fragments": 1277, "total_fragments": 1612, "gtdb_taxonomy": 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"d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_003610575.1", "gtdb_species": "s__Stappia sp003610575", "ani": 78.946, "matched_fragments": 537, "total_fragments": 1612, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.18", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_902502825.2", "gtdb_species": "s__Pseudorhizobium flavum", "ani": 77.9775, "matched_fragments": 224, "total_fragments": 1612, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudorhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.75", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.77", "num_clustered_genomes": 9, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": 0.301, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 33.0, "optimum_ph": null, "genome_size": 5436882.5, "gc_content": 63.432, "coding_genes": 5007.333, "rRNA16S_genes": 3.0, "tRNA_genes": 54.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 1.0, "psychrophilic_range_tmp": 0.0, "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": [ "Pannonibacter", "phragmitetus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }