{ "type": "genome", "identifier": "GCA_000802035.2", "organism": "[Pseudomonas] sp. BICA1-14", "title": "[Pseudomonas] sp. BICA1-14", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "EPFL", "publication": [ {} ], "properties": { "assembly_accession": "GCA_000802035.2", "bioproject": "PRJNA257561", "biosample": "SAMN02953435", "wgs_master": "JUEC00000000.2", "refseq_category": "na", "taxid": "1619235", "species_taxid": "1619235", "organism_name": "[Pseudomonas] sp. BICA1-14", "infraspecific_name": "", "isolate": "BICA1-14", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/07/02", "asm_name": "cluster c5", "submitter": "EPFL", "gbrs_paired_asm": "GCF_000802035.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/802/035/GCA_000802035.2_cluster_c5", "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": "2015-07-02", "dateModified": "2015-07-02", "datePublished": "2015-07-02", "_annotation": { "sample_count": 1, "sample_organism": [ "[Pseudomonas] sp. BICA1-14" ], "sample_taxid": [ "1619235" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Switzerland: Mt Terri URL, St-Ursanne" ], "sample_host_location_id": [], "data_size": "1.847 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "6579615", "Number of Sequences": "175", "Longest Sequences (bp)": "195462", "N50 (bp)": "90530", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.1", "Number of CDSs": "6044", "Average Protein Length": "314.8", "Coding Ratio (%)": "86.7", "Number of rRNAs": "6", "Number of tRNAs": "65", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_024397575.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 97.0237, "matched_fragments": 1395, "total_fragments": 2103, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_900114065.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 97.0035, "matched_fragments": 1407, "total_fragments": 2103, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Stutzerimonas chloritidismutans", "strain": "strain=AW-1", "accession": "GCA_000495915.1", "taxid": 203192, "species_taxid": 203192, "relation_to_type": "type", "validated": true, "ani": 96.9246, "matched_fragments": 1375, "total_fragments": 2103, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas songnenensis", "strain": "strain=DSM 27560T", "accession": "GCA_024448495.1", "taxid": 1176259, "species_taxid": 1176259, "relation_to_type": "type", "validated": true, "ani": 89.2541, "matched_fragments": 1274, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas songnenensis", "strain": "strain=NEAU-ST5-5", "accession": "GCA_003696315.1", "taxid": 1176259, "species_taxid": 1176259, "relation_to_type": "type", "validated": true, "ani": 89.2097, "matched_fragments": 1279, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=FDAARGOS_877", "accession": "GCA_016028515.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 89.09, "matched_fragments": 1279, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=DNSP21", "accession": "GCA_002890935.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 88.9318, "matched_fragments": 1291, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas stutzeri", "strain": "strain=CGMCC 1.1803", "accession": "GCA_000219605.1", "taxid": 316, "species_taxid": 316, "relation_to_type": "type", "validated": true, "ani": 87.9031, "matched_fragments": 1286, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas stutzeri", "strain": "strain=FDAARGOS_875", "accession": "GCA_016028655.1", "taxid": 316, "species_taxid": 316, "relation_to_type": "type", "validated": true, "ani": 87.8726, "matched_fragments": 1282, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sihuiensis", "strain": "strain=KCTC 32246", "accession": "GCA_900106015.1", "taxid": 1274359, "species_taxid": 1274359, "relation_to_type": "type", "validated": true, "ani": 80.7826, "matched_fragments": 812, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_013409135.1", "gtdb_species": "s__Pseudomonas_A kunmingensis_A", "ani": 97.2434, "matched_fragments": 1394, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.08, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "97.10", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "inconclusive" }, { "accession": "GCA_007713455.1", "gtdb_species": "s__Pseudomonas_A sp007713455", "ani": 97.15, "matched_fragments": 1371, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0636, "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": "inconclusive" }, { "accession": "GCF_003935375.1", "gtdb_species": "s__Pseudomonas_A xanthomarina_A", "ani": 97.0598, "matched_fragments": 1366, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0614, "mean_intra_species_ani": "97.25", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_002929225.1", "gtdb_species": "s__Pseudomonas_A stutzeri_U", "ani": 97.0462, "matched_fragments": 1418, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0711, "mean_intra_species_ani": "97.19", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900114065.1", "gtdb_species": "s__Pseudomonas_A kunmingensis", "ani": 97.0035, "matched_fragments": 1407, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.08, "mean_intra_species_ani": "97.31", "min_intra_species_ani": "97.18", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000495915.1", "gtdb_species": "s__Pseudomonas_A chloritidismutans", "ani": 96.9562, "matched_fragments": 1372, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 96.9847, "mean_intra_species_ani": "97.37", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_014764705.1", "gtdb_species": "s__Pseudomonas_A sp002692525", "ani": 96.9535, "matched_fragments": 1365, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0332, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_000935215.1", "gtdb_species": "s__Pseudomonas_A stutzeri_AD", "ani": 96.7292, "matched_fragments": 1281, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 96.8359, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "96.93", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_003488145.1", "gtdb_species": "s__Pseudomonas_A sp003488145", "ani": 96.4215, "matched_fragments": 874, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 96.7169, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.74", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000341615.1", "gtdb_species": "s__Pseudomonas_A stutzeri_G", "ani": 93.5653, "matched_fragments": 1313, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_015291885.1", "gtdb_species": "s__Pseudomonas_A stutzeri_AC", "ani": 89.3575, "matched_fragments": 1276, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "97.56", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003205815.1", "gtdb_species": "s__Pseudomonas_A sp003205815", "ani": 88.7394, "matched_fragments": 1302, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.18", "min_intra_species_ani": "96.58", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 27, "status": "-" }, { "accession": "GCF_000219605.1", "gtdb_species": "s__Pseudomonas_A stutzeri", "ani": 87.8908, "matched_fragments": 1287, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "96.98", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 156, "status": "-" }, { "accession": "GCF_000307775.2", "gtdb_species": "s__Pseudomonas_A stutzeri_B", "ani": 87.3671, "matched_fragments": 1202, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.65", "min_intra_species_ani": "98.65", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_008041835.1", "gtdb_species": "s__Pseudomonas_E sp002282595", "ani": 81.2607, "matched_fragments": 755, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.53", "min_intra_species_ani": "95.53", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.75", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900106015.1", "gtdb_species": "s__Pseudomonas_E sihuiensis", "ani": 80.7522, "matched_fragments": 818, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 96.7402, "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Pseudomonadaceae", "g__Stutzerimonas", "s__Stutzerimonas sp003530955" ], "_genome_taxon": [ "[Pseudomonas]", "sp.", "BICA1-14", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Pseudomonadaceae", "g__Stutzerimonas", "s__Stutzerimonas sp003530955", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Pseudomonadales", "Pseudomonadaceae", "Stutzerimonas", "Stutzerimonas", "sp003530955" ], "_meo": [ { "id": "MEO_0000036", "label": "water" }, { "id": "MEO_0000112", "label": "rock" } ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }