{ "type": "genome", "identifier": "GCA_004799515.1", "organism": "Phenylobacterium sp.", "title": "Phenylobacterium sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of Oklahoma", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004799515.1", "bioproject": "PRJNA521345", "biosample": "SAMN10882211", "wgs_master": "SSMX00000000.1", "refseq_category": "na", "taxid": "1871053", "species_taxid": "1871053", "organism_name": "Phenylobacterium sp.", "infraspecific_name": "", "isolate": "LY.12", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/17", "asm_name": "ASM479951v1", "submitter": "University of Oklahoma", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/799/515/GCA_004799515.1_ASM479951v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-17", "dateModified": "2019-04-17", "datePublished": "2019-04-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Phenylobacterium sp." ], "sample_taxid": [ "1871053" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA:Alaska" ], "sample_host_location_id": [], "data_size": "1.274 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.46, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4699331", "Number of Sequences": "56", "Longest Sequences (bp)": "500349", "N50 (bp)": "169079", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "69.5", "Number of CDSs": "4570", "Average Protein Length": "308.4", "Coding Ratio (%)": "90.0", "Number of rRNAs": "1", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phenylobacterium hankyongense", "strain": "strain=HKS-05", "accession": "GCA_003254505.1", "taxid": 1813876, "species_taxid": 1813876, "relation_to_type": "type", "validated": true, "ani": 83.1528, "matched_fragments": 799, "total_fragments": 1536, "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": 81.9165, "matched_fragments": 769, "total_fragments": 1536, "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": 81.4189, "matched_fragments": 754, "total_fragments": 1536, "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": 80.5538, "matched_fragments": 684, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium aquaticum", "strain": "strain=KACC 18306", "accession": "GCA_022695515.1", "taxid": 1763816, "species_taxid": 1763816, "relation_to_type": "type", "validated": true, "ani": 80.5524, "matched_fragments": 737, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium glaciei", "strain": "strain=20VBR1", "accession": "GCA_016772415.2", "taxid": 2803784, "species_taxid": 2803784, "relation_to_type": "type", "validated": true, "ani": 80.4385, "matched_fragments": 715, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phenylobacterium deserti", "strain": "strain=YIM 73061", "accession": "GCA_003254705.1", "taxid": 1914756, "species_taxid": 1914756, "relation_to_type": "type", "validated": true, "ani": 80.315, "matched_fragments": 592, "total_fragments": 1536, "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": 79.2807, "matched_fragments": 602, "total_fragments": 1536, "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": 79.0931, "matched_fragments": 609, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Caulobacter vibrioides", "strain": "strain=DSM 9893", "accession": "GCA_002858865.1", "taxid": 155892, "species_taxid": 155892, "relation_to_type": "type", "validated": true, "ani": 78.8135, "matched_fragments": 497, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevundimonas albigilva", "strain": "strain=KEME 9005-016", "accession": "GCA_023503965.1", "taxid": 1312364, "species_taxid": 1312364, "relation_to_type": "type", "validated": true, "ani": 78.2982, "matched_fragments": 420, "total_fragments": 1536, "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": 78.1575, "matched_fragments": 335, "total_fragments": 1536, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.46, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_004799515.1", "gtdb_species": "s__Phenylobacterium sp004799515", "ani": 100.0, "matched_fragments": 1529, "total_fragments": 1536, "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_018241625.1", "gtdb_species": "s__Phenylobacterium sp018241625", "ani": 85.1816, "matched_fragments": 836, "total_fragments": 1536, "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_004799395.1", "gtdb_species": "s__Phenylobacterium sp004799395", "ani": 84.7442, "matched_fragments": 947, "total_fragments": 1536, "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_903822175.1", "gtdb_species": "s__Phenylobacterium sp903822175", "ani": 84.6059, "matched_fragments": 1009, "total_fragments": 1536, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.88", "min_intra_species_ani": "99.77", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_003136395.1", "gtdb_species": "s__Phenylobacterium sp003136395", "ani": 83.9159, "matched_fragments": 892, "total_fragments": 1536, "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": 83.1318, "matched_fragments": 801, "total_fragments": 1536, "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": 82.3353, "matched_fragments": 851, "total_fragments": 1536, "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_004297125.1", "gtdb_species": "s__Phenylobacterium sp004297125", "ani": 81.2287, "matched_fragments": 796, "total_fragments": 1536, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Caulobacterales", "f__Caulobacteraceae", "g__Phenylobacterium", "s__Phenylobacterium sp004799515" ], "_genome_taxon": [ "Phenylobacterium", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Caulobacterales", "f__Caulobacteraceae", "g__Phenylobacterium", "s__Phenylobacterium sp004799515", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Caulobacterales", "Caulobacteraceae", "Phenylobacterium", "Phenylobacterium", "sp004799515" ], "_meo": [ { "id": "MEO_0000007", "label": "soil" }, { "id": "MEO_0000814", "label": "tundra" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }