{ "type": "genome", "identifier": "GCF_016772415.1", "organism": "Phenylobacterium glaciei", "title": "Phenylobacterium glaciei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "NCPOR", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016772415.1", "bioproject": "PRJNA224116", "biosample": "SAMN17312737", "wgs_master": "JAGSGD000000000.1", "refseq_category": "reference genome", "taxid": "2803784", "species_taxid": "2803784", "organism_name": "Phenylobacterium glaciei", "infraspecific_name": "strain=20VBR1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/24", "asm_name": "ASM1677241v2", "asm_submitter": "NCPOR", "gbrs_paired_asm": "GCA_016772415.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/772/415/GCF_016772415.1_ASM1677241v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4242328", "genome_size_ungapped": "4242328", "gc_percent": "68.000000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016772415.1-RS_2024_05_26", "annotation_date": "2024-05-26", "total_gene_count": "4194", "protein_coding_gene_count": "4124", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-24", "dateModified": "2021-04-24", "datePublished": "2021-04-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Phenylobacterium glaciei" ], "sample_taxid": [ "2803784" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Svalbard:Ny-Alesund" ], "sample_host_location_id": [], "data_size": "1.156 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4242328", "Number of Sequences": "5", "Longest Sequences (bp)": "3821543", "N50 (bp)": "3821543", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.9", "Number of CDSs": "4182", "Average Protein Length": "306.5", "Coding Ratio (%)": "90.6", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phenylobacterium glaciei", "strain": "strain=20VBR1", "accession": "GCA_016772415.2", "taxid": 2803784, "species_taxid": 2803784, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1411, "total_fragments": 1411, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Phenylobacterium aquaticum", "strain": "strain=KACC 18306", "accession": "GCA_022695515.1", "taxid": 1763816, "species_taxid": 1763816, "relation_to_type": "type", "validated": true, "ani": 82.443, "matched_fragments": 930, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium hankyongense", "strain": "strain=HKS-05", "accession": "GCA_003254505.1", "taxid": 1813876, "species_taxid": 1813876, "relation_to_type": "type", "validated": true, "ani": 81.4283, "matched_fragments": 736, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium haematophilum", "strain": "strain=DSM 21793", "accession": "GCA_014196295.1", "taxid": 98513, "species_taxid": 98513, "relation_to_type": "type", "validated": true, "ani": 80.9571, "matched_fragments": 766, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium soli", "strain": "strain=LX32", "accession": "GCA_003254475.1", "taxid": 2170551, "species_taxid": 2170551, "relation_to_type": "type", "validated": true, "ani": 80.4386, "matched_fragments": 685, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium zucineum", "strain": "strain=HLK1", "accession": "GCA_000017265.1", "taxid": 284016, "species_taxid": 284016, "relation_to_type": "type", "validated": true, "ani": 80.2575, "matched_fragments": 714, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium kunshanense", "strain": "strain=BUT-10", "accession": "GCA_003254525.1", "taxid": 1445034, "species_taxid": 1445034, "relation_to_type": "type", "validated": true, "ani": 79.7346, "matched_fragments": 636, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter rhizosphaerae", "strain": "strain=KCTC 52515", "accession": "GCA_010977555.1", "taxid": 2010972, "species_taxid": 2010972, "relation_to_type": "type", "validated": true, "ani": 79.4559, "matched_fragments": 652, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter soli", "strain": "strain=Ji-3-8", "accession": "GCA_011045195.1", "taxid": 2708539, "species_taxid": 2708539, "relation_to_type": "type", "validated": true, "ani": 79.391, "matched_fragments": 664, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter rhizosphaerae", "strain": "strain=CGMCC 1.15915", "accession": "GCA_014645055.1", "taxid": 2010972, "species_taxid": 2010972, "relation_to_type": "type", "validated": true, "ani": 79.3708, "matched_fragments": 644, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter radicis", "strain": "strain=695", "accession": "GCA_003094615.1", "taxid": 2172650, "species_taxid": 2172650, "relation_to_type": "type", "validated": true, "ani": 79.3045, "matched_fragments": 650, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter mirabilis", "strain": "strain=FWC 38", "accession": "GCA_002749615.1", "taxid": 69666, "species_taxid": 69666, "relation_to_type": "type", "validated": true, "ani": 79.2834, "matched_fragments": 621, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas guildfordensis", "strain": "strain=Sa3CVA3", "accession": "GCA_014836405.1", "taxid": 2762241, "species_taxid": 2762241, "relation_to_type": "type", "validated": true, "ani": 78.052, "matched_fragments": 339, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Starkeya koreensis", "strain": "strain=Jip08", "accession": "GCA_023016525.1", "taxid": 266121, "species_taxid": 266121, "relation_to_type": "type", "validated": true, "ani": 76.4674, "matched_fragments": 211, "total_fragments": 1411, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016772415.1", "gtdb_species": "s__Phenylobacterium sp016772415", "ani": 100.0, "matched_fragments": 1411, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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": "GCA_018001015.1", "gtdb_species": "s__Phenylobacterium sp018001015", "ani": 89.1429, "matched_fragments": 1067, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.70", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001429025.1", "gtdb_species": "s__Phenylobacterium sp001429025", "ani": 81.94, "matched_fragments": 806, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.02", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018240795.1", "gtdb_species": "s__Phenylobacterium sp018240795", "ani": 81.4294, "matched_fragments": 696, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_003254505.1", "gtdb_species": "s__Phenylobacterium hankyongense", "ani": 81.4184, "matched_fragments": 737, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_017991675.1", "gtdb_species": "s__Phenylobacterium sp017991675", "ani": 81.3751, "matched_fragments": 530, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_001425305.1", "gtdb_species": "s__Phenylobacterium sp001425305", "ani": 81.3362, "matched_fragments": 769, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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": 3, "status": "-" }, { "accession": "GCA_013822795.1", "gtdb_species": "s__Phenylobacterium sp013822795", "ani": 81.1603, "matched_fragments": 778, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_004799545.1", "gtdb_species": "s__Phenylobacterium sp004799545", "ani": 80.6457, "matched_fragments": 686, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_004799515.1", "gtdb_species": "s__Phenylobacterium sp004799515", "ani": 80.5838, "matched_fragments": 706, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_003254475.1", "gtdb_species": "s__Phenylobacterium soli", "ani": 80.4507, "matched_fragments": 684, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_018241625.1", "gtdb_species": "s__Phenylobacterium sp018241625", "ani": 80.3456, "matched_fragments": 583, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_018821435.1", "gtdb_species": "s__Phenylobacterium sp018821435", "ani": 80.1738, "matched_fragments": 732, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000281955.1", "gtdb_species": "s__Caulobacter sp000281955", "ani": 79.683, "matched_fragments": 635, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter", "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_001375595.1", "gtdb_species": "s__Phenylobacterium immobile", "ani": 79.372, "matched_fragments": 436, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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_903909375.1", "gtdb_species": "s__Phenylobacterium sp903909375", "ani": 79.0217, "matched_fragments": 515, "total_fragments": 1411, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "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": -0.244, "cell_length": 0.056, "doubling_h": 0.875, "growth_tmp": 31.25, "optimum_tmp": 32.375, "optimum_ph": 6.916, "genome_size": 3316466.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.5, "range_salinity": null, "facultative_respiration": 0.166, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.833, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.75, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.25, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Phenylobacterium", "glaciei" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }