{ "type": "genome", "identifier": "GCF_014773225.1", "organism": "Pontibacter aquaedesilientis", "title": "Pontibacter aquaedesilientis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Dongguk University, Biomedi Campus", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014773225.1", "bioproject": "PRJNA224116", "biosample": "SAMN16072476", "wgs_master": "JACXAJ000000000.1", "refseq_category": "reference genome", "taxid": "2766980", "species_taxid": "2766980", "organism_name": "Pontibacter aquaedesilientis", "infraspecific_name": "strain=JH31", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/21", "asm_name": "ASM1477322v1", "asm_submitter": "Dongguk University, Biomedi Campus", "gbrs_paired_asm": "GCA_014773225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/773/225/GCF_014773225.1_ASM1477322v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4117105", "genome_size_ungapped": "4117105", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014773225.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3601", "protein_coding_gene_count": "3539", "non_coding_gene_count": "49", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-21", "dateModified": "2020-09-21", "datePublished": "2020-09-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Pontibacter aquaedesilientis" ], "sample_taxid": [ "2766980" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.177 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.44, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4117105", "Number of Sequences": "18", "Longest Sequences (bp)": "1162657", "N50 (bp)": "375132", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.7", "Number of CDSs": "3550", "Average Protein Length": "335.2", "Coding Ratio (%)": "86.7", "Number of rRNAs": "3", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pontibacter aquaedesilientis", "strain": "strain=JH31", "accession": "GCA_014773225.1", "taxid": 2766980, "species_taxid": 2766980, 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81.2376, "matched_fragments": 825, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter ramchanderi", "strain": "strain=LP43", "accession": "GCA_002846395.1", "taxid": 1179743, "species_taxid": 1179743, "relation_to_type": "type", "validated": true, "ani": 81.1835, "matched_fragments": 819, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter indicus", "strain": "strain=LP100", "accession": "GCA_900156345.1", "taxid": 1317125, "species_taxid": 1317125, "relation_to_type": "type", "validated": true, "ani": 81.0317, "matched_fragments": 832, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter roseus", "strain": "strain=DSM 17521", "accession": "GCA_000373265.1", "taxid": 336989, "species_taxid": 336989, "relation_to_type": "type", "validated": true, "ani": 80.1729, "matched_fragments": 742, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter ruber", "strain": "strain=JC213", "accession": "GCA_023630205.1", "taxid": 1343895, "species_taxid": 1343895, "relation_to_type": "type", "validated": true, "ani": 78.7319, "matched_fragments": 523, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter deserti", "strain": "strain=JC215", "accession": "GCA_023630255.1", "taxid": 1343896, "species_taxid": 1343896, "relation_to_type": "type", "validated": true, "ani": 78.1348, "matched_fragments": 310, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter pamirensis", "strain": "strain=TRT317", "accession": "GCA_010015475.1", "taxid": 2562824, "species_taxid": 2562824, "relation_to_type": "type", "validated": true, "ani": 77.5914, "matched_fragments": 336, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rufibacter sediminis", "strain": "strain=CGMCC 1.16289", "accession": "GCA_024436355.1", "taxid": 2762756, "species_taxid": 2762756, "relation_to_type": "type", "validated": true, "ani": 76.4804, "matched_fragments": 147, "total_fragments": 1362, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.44, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014773225.1", "gtdb_species": "s__Pontibacter sp014773225", "ani": 100.0, "matched_fragments": 1360, "total_fragments": 1362, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_014638845.1", "gtdb_species": "s__Pontibacter amylolyticus", "ani": 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1362, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_002846395.1", "gtdb_species": "s__Pontibacter ramchanderi", "ani": 81.1721, "matched_fragments": 821, "total_fragments": 1362, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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_015686655.1", "gtdb_species": "s__Pontibacter sp015686655", "ani": 81.1607, "matched_fragments": 823, "total_fragments": 1362, "gtdb_taxonomy": 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"d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "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": -0.236, "cell_length": 0.229, "doubling_h": null, "growth_tmp": 28.5, "optimum_tmp": 29.924, "optimum_ph": 7.3, "genome_size": 4957048.166, "gc_content": 51.009, "coding_genes": 4209.666, "rRNA16S_genes": 4.0, "tRNA_genes": 46.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.363, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "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": [ "Pontibacter", "aquaedesilientis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }