{ "type": "genome", "identifier": "GCA_018780705.1", "organism": "Pseudomonas sp.", "title": "Pseudomonas sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "Friedrich Schiller University Jena", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018780705.1", "bioproject": "PRJNA633367", "biosample": "SAMN16635726", "wgs_master": "JADMJI000000000.1", "refseq_category": "na", "taxid": "306", "species_taxid": "306", "organism_name": "Pseudomonas sp.", "infraspecific_name": "", "isolate": "MAG_21", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/06/08", "asm_name": "ASM1878070v1", "submitter": "Friedrich Schiller University Jena", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/780/705/GCA_018780705.1_ASM1878070v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-06-08", "dateModified": "2021-06-08", "datePublished": "2021-06-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas sp." ], "sample_taxid": [ "306" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Hainich National Park, Hainich Critical Zone Exploratory" ], "sample_host_location_id": [], "data_size": "0.974 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 65.66, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3375217", "Number of Sequences": "1252", "Longest Sequences (bp)": "26644", "N50 (bp)": "3191", "Gap Ratio (%)": "0.241910", "GCcontent (%)": "62.5", "Number of CDSs": "2122", "Average Protein Length": "276.1", "Coding Ratio (%)": "52.1", "Number of rRNAs": "1", "Number of tRNAs": "31", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas campi", "strain": "strain=S1-A32-2", "accession": "GCA_013200955.2", "taxid": 2731681, "species_taxid": 2731681, "relation_to_type": "type", "validated": true, "ani": 81.9305, "matched_fragments": 313, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas guryensis", "strain": "strain=SR9", "accession": "GCA_014164785.1", "taxid": 2759165, "species_taxid": 2759165, "relation_to_type": "type", "validated": true, "ani": 81.6559, "matched_fragments": 320, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas tumuqii", "strain": "strain=LAMW06", "accession": "GCA_013184545.1", "taxid": 2715755, "species_taxid": 2715755, "relation_to_type": "type", "validated": true, "ani": 81.6101, "matched_fragments": 291, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas ullengensis", "strain": "strain=UL070", "accession": "GCA_014174475.1", "taxid": 2759166, "species_taxid": 2759166, "relation_to_type": "type", "validated": true, "ani": 81.3827, "matched_fragments": 315, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 81.3675, "matched_fragments": 294, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas borbori", "strain": "strain=DSM 17834", "accession": "GCA_900115555.1", "taxid": 289003, "species_taxid": 289003, "relation_to_type": "type", "validated": true, "ani": 81.3179, "matched_fragments": 292, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas tohonis", "strain": "strain=TUM18999", "accession": "GCA_012767755.2", "taxid": 2725477, "species_taxid": 2725477, "relation_to_type": "type", "validated": true, "ani": 81.2399, "matched_fragments": 314, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cavernae", "strain": "strain=K2W31S-8", "accession": "GCA_003595175.1", "taxid": 2320867, "species_taxid": 2320867, "relation_to_type": "type", "validated": true, "ani": 81.1581, "matched_fragments": 308, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas peli", "strain": "strain=DSM 17833", "accession": "GCA_012986145.1", "taxid": 592361, "species_taxid": 592361, "relation_to_type": "type", "validated": true, "ani": 81.0687, "matched_fragments": 292, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas peli", "strain": "strain=DSM 17833", "accession": "GCA_900099645.1", "taxid": 592361, "species_taxid": 592361, "relation_to_type": "type", "validated": true, "ani": 81.0466, "matched_fragments": 292, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cuatrocienegasensis", "strain": "strain=CIP 109853", "accession": "GCA_900110925.1", "taxid": 543360, "species_taxid": 543360, "relation_to_type": "type", "validated": true, "ani": 80.9138, "matched_fragments": 275, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas insulae", "strain": "strain=UL073", "accession": "GCA_016901015.1", "taxid": 2809017, "species_taxid": 2809017, "relation_to_type": "type", "validated": true, "ani": 80.9057, "matched_fragments": 297, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas otitidis", "strain": "strain=DSM 17224", "accession": "GCA_900111835.1", "taxid": 319939, "species_taxid": 319939, "relation_to_type": "suspected-type", "validated": true, "ani": 80.7256, "matched_fragments": 309, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cavernicola", "strain": "strain=K1S02-6", "accession": "GCA_003596405.1", "taxid": 2320866, "species_taxid": 2320866, "relation_to_type": "type", "validated": true, "ani": 80.5545, "matched_fragments": 282, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kuykendallii", "strain": "strain=NRRL B-59562", "accession": "GCA_900106975.1", "taxid": 1007099, "species_taxid": 1007099, "relation_to_type": "type", "validated": true, "ani": 80.4867, "matched_fragments": 262, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_019823065.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 80.1235, "matched_fragments": 228, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mosselii", "strain": "strain=DSM 17497", "accession": "GCA_000621225.1", "taxid": 78327, "species_taxid": 78327, "relation_to_type": "type", "validated": true, "ani": 80.1129, "matched_fragments": 228, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_013373935.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 80.0346, "matched_fragments": 233, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas iranensis", "strain": "strain=SWRI54", "accession": "GCA_014268585.2", "taxid": 2745503, "species_taxid": 2745503, "relation_to_type": "type", "validated": true, "ani": 80.015, "matched_fragments": 211, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas siliginis", "strain": "strain=SWRI31", "accession": "GCA_019145195.1", "taxid": 2842346, "species_taxid": 2842346, "relation_to_type": "type", "validated": true, "ani": 79.9385, "matched_fragments": 213, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas yamanorum", "strain": "strain=LMG 27247", "accession": "GCA_900105735.1", "taxid": 515393, "species_taxid": 515393, "relation_to_type": "suspected-type", "validated": true, "ani": 79.9031, "matched_fragments": 229, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas paralactis", "strain": "strain=DSM 29164", "accession": "GCA_001439735.1", "taxid": 1615673, "species_taxid": 1615673, "relation_to_type": "type", "validated": true, "ani": 79.8087, "matched_fragments": 197, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas guineae", "strain": "strain=LMG 24016", "accession": "GCA_900113745.1", "taxid": 425504, "species_taxid": 425504, "relation_to_type": "type", "validated": true, "ani": 79.7016, "matched_fragments": 256, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas extremorientalis", "strain": "strain=CCUG 51517", "accession": "GCA_008801565.1", "taxid": 169669, "species_taxid": 169669, "relation_to_type": "type", "validated": true, "ani": 79.5759, "matched_fragments": 216, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas extremorientalis", "strain": "", "accession": "GCA_900625005.1", "taxid": 169669, "species_taxid": 169669, "relation_to_type": "type", "validated": true, "ani": 79.5444, "matched_fragments": 219, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas extremorientalis", "strain": "strain=LMG 19695", "accession": "GCA_001870465.1", "taxid": 169669, "species_taxid": 169669, "relation_to_type": "type", "validated": true, "ani": 79.5239, "matched_fragments": 218, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Pseudomonas] nosocomialis", "strain": "strain=A31/70", "accession": "GCA_005876855.1", "taxid": 1056496, "species_taxid": 1056496, "relation_to_type": "type", "validated": true, "ani": 79.4955, "matched_fragments": 204, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas azotifigens", "strain": "strain=DSM 17556", "accession": "GCA_000425625.1", "taxid": 291995, "species_taxid": 291995, "relation_to_type": "type", "validated": true, "ani": 79.4642, "matched_fragments": 217, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azotoformans", "strain": "strain=NBRC 12693", "accession": "GCA_002091515.1", "taxid": 47878, "species_taxid": 47878, "relation_to_type": "suspected-type", "validated": true, "ani": 79.4242, "matched_fragments": 232, "total_fragments": 471, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 65.66, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009799925.1", "gtdb_species": "s__Pseudomonas_E sp009799925", "ani": 82.435, "matched_fragments": 316, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_902506505.1", "gtdb_species": "s__Pseudomonas_E sp902506505", "ani": 82.2284, "matched_fragments": 311, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.45", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013200955.2", "gtdb_species": "s__Pseudomonas_E campi", "ani": 81.9535, "matched_fragments": 312, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_014164785.1", "gtdb_species": "s__Pseudomonas_E sp014164785", "ani": 81.6559, "matched_fragments": 320, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_002840155.1", "gtdb_species": "s__Pseudomonas_E sp002840155", "ani": 81.6071, "matched_fragments": 292, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_002354655.1", "gtdb_species": "s__Pseudomonas_E sp002354655", "ani": 81.5967, "matched_fragments": 302, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013184545.1", "gtdb_species": "s__Pseudomonas_E sp013184545", "ani": 81.5861, "matched_fragments": 292, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_014174475.1", "gtdb_species": "s__Pseudomonas_E sp014174475", "ani": 81.4266, "matched_fragments": 313, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_018398425.1", "gtdb_species": "s__Pseudomonas_E lalucatii", "ani": 81.3909, "matched_fragments": 293, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.68", "min_intra_species_ani": "99.28", "mean_intra_species_af": "0.97", "min_intra_species_af": 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1, "status": "-" }, { "accession": "GCF_009763245.1", "gtdb_species": "s__Pseudomonas_E sp009763245", "ani": 81.0632, "matched_fragments": 293, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_900099645.1", "gtdb_species": "s__Pseudomonas_E peli", "ani": 81.0466, "matched_fragments": 292, "total_fragments": 471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.85", "min_intra_species_ani": "96.04", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { 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