{ "type": "genome", "identifier": "GCF_023630255.1", "organism": "Pontibacter deserti", "title": "Pontibacter deserti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ningbo University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023630255.1", "bioproject": "PRJNA224116", "biosample": "SAMN26106925", "wgs_master": "JALPRS000000000.1", "refseq_category": "reference genome", "taxid": "1343896", "species_taxid": "1343896", "organism_name": "Pontibacter deserti", "infraspecific_name": "strain=JC215", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/06/01", "asm_name": "ASM2363025v1", "asm_submitter": "Ningbo University", "gbrs_paired_asm": "GCA_023630255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/630/255/GCF_023630255.1_ASM2363025v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4149358", "genome_size_ungapped": "4149358", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023630255.1-RS_2024_10_25", "annotation_date": "2024-10-25", "total_gene_count": "3661", "protein_coding_gene_count": "3604", "non_coding_gene_count": "45", "pubmed_id": "24425823" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-06-01", "dateModified": "2022-06-01", "datePublished": "2022-06-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Pontibacter deserti" ], "sample_taxid": [ "1343896" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Gujarat" ], "sample_host_location_id": [], "data_size": "1.178 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)": "4149358", "Number of Sequences": "7", "Longest Sequences (bp)": "2718985", "N50 (bp)": "2718985", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.9", "Number of CDSs": "3613", "Average Protein Length": "332.5", "Coding Ratio (%)": "86.8", "Number of rRNAs": "3", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pontibacter deserti", "strain": "strain=JC215", "accession": "GCA_023630255.1", "taxid": 1343896, "species_taxid": 1343896, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1380, "total_fragments": 1380, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pontibacter fetidus", "strain": "strain=BT213", "accession": "GCA_010119545.1", "taxid": 2700082, "species_taxid": 2700082, "relation_to_type": "type", "validated": true, "ani": 82.625, "matched_fragments": 875, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter pudoricolor", "strain": "strain=BT214", "accession": "GCA_010092985.1", "taxid": 2694930, "species_taxid": 2694930, "relation_to_type": "type", "validated": true, "ani": 82.0079, "matched_fragments": 866, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter burrus", "strain": "strain=BT327", "accession": "GCA_010686685.1", "taxid": 2704466, "species_taxid": 2704466, "relation_to_type": "type", "validated": true, "ani": 80.9596, "matched_fragments": 728, "total_fragments": 1380, "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": 79.1667, "matched_fragments": 524, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter lucknowensis", "strain": "strain=DM9", "accession": "GCA_900156415.1", "taxid": 1077936, "species_taxid": 1077936, "relation_to_type": "type", "validated": true, "ani": 78.2527, "matched_fragments": 325, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter arcticus", "strain": "strain=2b14", "accession": "GCA_003284895.1", "taxid": 2080288, "species_taxid": 2080288, "relation_to_type": "type", "validated": true, "ani": 78.2184, "matched_fragments": 425, "total_fragments": 1380, "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": 78.1327, "matched_fragments": 351, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter mangrovi", "strain": "strain=HB172049", "accession": "GCA_006385705.1", "taxid": 2589816, "species_taxid": 2589816, "relation_to_type": "type", "validated": true, "ani": 78.13, "matched_fragments": 372, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter aquaedesilientis", "strain": "strain=JH31", "accession": "GCA_014773225.1", "taxid": 2766980, "species_taxid": 2766980, "relation_to_type": "type", "validated": true, "ani": 77.9645, "matched_fragments": 328, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pontibacter chinhatensis", "strain": "strain=LP51", "accession": "GCA_900113285.1", "taxid": 1436961, "species_taxid": 1436961, "relation_to_type": "type", "validated": true, "ani": 77.7829, "matched_fragments": 374, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014297265.1", "gtdb_species": "s__Pontibacter sp014297265", "ani": 99.9987, "matched_fragments": 1377, "total_fragments": 1380, "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_010119545.1", "gtdb_species": "s__Pontibacter fetidus", "ani": 82.6489, "matched_fragments": 872, "total_fragments": 1380, "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_010092985.1", "gtdb_species": "s__Pontibacter pudoricolor", "ani": 82.0056, "matched_fragments": 867, "total_fragments": 1380, "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": "GCA_018122615.1", "gtdb_species": "s__Pontibacter sp018122615", "ani": 82.0016, "matched_fragments": 867, "total_fragments": 1380, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014212495.1", "gtdb_species": "s__Pontibacter sp014212495", "ani": 81.2925, "matched_fragments": 801, "total_fragments": 1380, "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_010686685.1", "gtdb_species": "s__Pontibacter burrus", "ani": 80.942, "matched_fragments": 731, "total_fragments": 1380, "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_900156345.1", "gtdb_species": "s__Pontibacter indicus", "ani": 78.1098, "matched_fragments": 352, "total_fragments": 1380, "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": "-" } ] }, "_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", "deserti" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }