{ "type": "genome", "identifier": "GCF_020532745.1", "organism": "Polaribacter porphyrae", "title": "Polaribacter porphyrae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "GEOMAR Helmholtz Center for Ocean Research Kiel", "publication": [ {} ], "properties": { "assembly_accession": "GCF_020532745.1", "bioproject": "PRJNA224116", "biosample": "SAMN12419157", "wgs_master": "VRMK00000000.1", "refseq_category": "na", "taxid": "1137780", "species_taxid": "1137780", "organism_name": "Polaribacter porphyrae", "infraspecific_name": "strain=LMG 26671", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/10/19", "asm_name": "ASM2053274v1", "asm_submitter": "GEOMAR Helmholtz Center for Ocean Research Kiel", "gbrs_paired_asm": "GCA_020532745.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/532/745/GCF_020532745.1_ASM2053274v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3899394", "genome_size_ungapped": "3899394", "gc_percent": "29.000000", "replicon_count": "0", "scaffold_count": "29", "contig_count": "29", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_020532745.1-RS_2024_08_04", "annotation_date": "2024-08-04", "total_gene_count": "3541", "protein_coding_gene_count": "3472", "non_coding_gene_count": "41", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-10-19", "dateModified": "2021-10-19", "datePublished": "2021-10-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Polaribacter porphyrae" ], "sample_taxid": [ "1137780" ], "sample_host_organism": [ "Porphyrae yezoensis (red alga)" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan: sea near Kisarazu" ], "sample_host_location_id": [], "data_size": "1.058 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)": "3899394", "Number of Sequences": "29", "Longest Sequences (bp)": "952385", "N50 (bp)": "504188", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.1", "Number of CDSs": "3496", "Average Protein Length": "339.7", "Coding Ratio (%)": "91.4", "Number of rRNAs": "3", "Number of tRNAs": "34", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Polaribacter porphyrae", "strain": "strain=LMG 26671", "accession": "GCA_020532745.1", "taxid": 1137780, "species_taxid": 1137780, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1289, "total_fragments": 1289, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Polaribacter porphyrae", "strain": "strain=NBRC 108759", "accession": "GCA_002954685.1", "taxid": 1137780, "species_taxid": 1137780, "relation_to_type": "type", "validated": true, "ani": 99.9933, "matched_fragments": 1287, "total_fragments": 1289, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Polaribacter reichenbachii", "strain": "strain=LMG 26443", "accession": "GCA_020532845.1", "taxid": 996801, "species_taxid": 996801, "relation_to_type": "type", "validated": true, "ani": 81.1339, "matched_fragments": 700, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter reichenbachii", "strain": "strain=KCTC 23969", "accession": "GCA_001680875.1", "taxid": 996801, "species_taxid": 996801, "relation_to_type": "type", "validated": true, "ani": 81.1086, "matched_fragments": 707, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter reichenbachii", "strain": "strain=KCTC 23969", "accession": "GCA_002814055.1", "taxid": 996801, "species_taxid": 996801, "relation_to_type": "type", "validated": true, "ani": 81.0174, "matched_fragments": 716, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter vadi", "strain": "strain=LPB0003", "accession": "GCA_001761365.1", "taxid": 1774273, "species_taxid": 1774273, "relation_to_type": "type", "validated": true, "ani": 80.8926, "matched_fragments": 706, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter vadi", "strain": "strain=LPB0003", "accession": "GCA_001680885.1", "taxid": 1774273, "species_taxid": 1774273, "relation_to_type": "type", "validated": true, "ani": 80.8608, "matched_fragments": 716, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter dokdonensis", "strain": "strain=DSW-5", "accession": "GCA_001280865.1", "taxid": 326329, "species_taxid": 326329, "relation_to_type": "type", "validated": true, "ani": 80.4627, "matched_fragments": 619, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter dokdonensis", "strain": "strain=DSW-5", "accession": "GCA_900106865.1", "taxid": 326329, "species_taxid": 326329, "relation_to_type": "type", "validated": true, "ani": 80.4413, "matched_fragments": 625, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter dokdonensis", "strain": "strain=KCTC 12392", "accession": "GCA_024362345.1", "taxid": 326329, "species_taxid": 326329, "relation_to_type": "type", "validated": true, "ani": 80.4239, "matched_fragments": 631, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter pectinis", "strain": "strain=L12M9", "accession": "GCA_014352875.1", "taxid": 2738844, "species_taxid": 2738844, "relation_to_type": "type", "validated": true, "ani": 80.3427, "matched_fragments": 633, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter septentrionalilitoris", "strain": "strain=ANORD1", "accession": "GCA_009832745.1", "taxid": 2494657, "species_taxid": 2494657, "relation_to_type": "type", "validated": true, "ani": 80.2701, "matched_fragments": 608, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter cellanae", "strain": "strain=SM13", "accession": "GCA_017569185.1", "taxid": 2818493, "species_taxid": 2818493, "relation_to_type": "type", "validated": true, "ani": 79.7552, "matched_fragments": 587, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polaribacter batillariae", "strain": "strain=G4M1", "accession": "GCA_017498485.1", "taxid": 2808900, "species_taxid": 2808900, "relation_to_type": "type", "validated": true, "ani": 79.3883, "matched_fragments": 582, "total_fragments": 1289, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002954685.1", "gtdb_species": "s__Polaribacter porphyrae", "ani": 99.9933, "matched_fragments": 1287, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_018861005.1", "gtdb_species": "s__Polaribacter vadi_A", "ani": 81.0346, "matched_fragments": 720, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_001975665.1", "gtdb_species": "s__Polaribacter reichenbachii", "ani": 80.997, "matched_fragments": 721, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001761365.1", "gtdb_species": "s__Polaribacter vadi", "ani": 80.888, "matched_fragments": 707, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_001280865.1", "gtdb_species": "s__Polaribacter dokdonensis", "ani": 80.4438, "matched_fragments": 621, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_900105145.1", "gtdb_species": "s__Polaribacter sp900105145", "ani": 80.3593, "matched_fragments": 647, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_000766795.1", "gtdb_species": "s__Polaribacter sp000766795", "ani": 80.3253, "matched_fragments": 634, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_003129485.1", "gtdb_species": "s__Polaribacter sp003129485", "ani": 80.2709, "matched_fragments": 596, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_009832745.1", "gtdb_species": "s__Polaribacter sp009832745", "ani": 80.2527, "matched_fragments": 610, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_000152945.2", "gtdb_species": "s__Polaribacter sp000152945", "ani": 80.1396, "matched_fragments": 610, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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_014784055.1", "gtdb_species": "s__Polaribacter haliotis", "ani": 80.0358, "matched_fragments": 624, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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": "GCA_905480405.1", "gtdb_species": "s__Polaribacter sp905480405", "ani": 79.9444, "matched_fragments": 568, "total_fragments": 1289, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter", "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": -0.432, "cell_length": 0.143, "doubling_h": null, "growth_tmp": 9.75, "optimum_tmp": 25.0, "optimum_ph": 7.0, "genome_size": 4097747.844, "gc_content": 31.525, "coding_genes": 3329.75, "rRNA16S_genes": 3.0, "tRNA_genes": 41.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 1.0, "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": [ "Polaribacter", "porphyrae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }