{ "type": "genome", "identifier": "GCF_019145435.1", "organism": "Pseudomonas ekonensis", "title": "Pseudomonas ekonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "KU Leuven", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019145435.1", "bioproject": "PRJNA224116", "biosample": "SAMN19473669", "wgs_master": "JAHSTS000000000.1", "refseq_category": "reference genome", "taxid": "2842353", "species_taxid": "2842353", "organism_name": "Pseudomonas ekonensis", "infraspecific_name": "strain=COR58", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/06", "asm_name": "ASM1914543v1", "asm_submitter": "KU Leuven", "gbrs_paired_asm": "GCA_019145435.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/145/435/GCF_019145435.1_ASM1914543v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6133900", "genome_size_ungapped": "6133900", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "7", "contig_count": "7", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019145435.1-RS_2024_07_22", "annotation_date": "2024-07-22", "total_gene_count": "5505", "protein_coding_gene_count": "5386", "non_coding_gene_count": "85", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-06", "dateModified": "2021-07-06", "datePublished": "2021-07-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas ekonensis" ], "sample_taxid": [ "2842353" ], "sample_host_organism": [ "Xanthosoma sagittifolium" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Cameroon: Ekona" ], "sample_host_location_id": [], "data_size": "1.677 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6133900", "Number of Sequences": "7", "Longest Sequences (bp)": "2933681", "N50 (bp)": "2432822", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.9", "Number of CDSs": "5441", "Average Protein Length": "334.4", "Coding Ratio (%)": "89.0", "Number of rRNAs": "14", "Number of tRNAs": "72", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas ekonensis", "strain": "strain=COR58", "accession": "GCA_019145435.1", "taxid": 2842353, "species_taxid": 2842353, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2041, "total_fragments": 2041, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas sputi", "strain": "strain=BML-PP014", "accession": "GCA_021603585.1", "taxid": 2892325, "species_taxid": 2892325, "relation_to_type": "type", "validated": true, "ani": 88.3449, "matched_fragments": 1594, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pharyngis", "strain": "strain=BML-PP036", "accession": "GCA_021602345.1", "taxid": 2892333, "species_taxid": 2892333, "relation_to_type": "type", "validated": true, "ani": 88.3417, "matched_fragments": 1630, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kribbensis", "strain": "strain=46-2", "accession": "GCA_003352185.1", "taxid": 1628086, "species_taxid": 1628086, "relation_to_type": "type", "validated": true, "ani": 88.3182, "matched_fragments": 1673, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas allokribbensis", "strain": "strain=IzPS23", "accession": "GCA_014863605.1", "taxid": 2774460, "species_taxid": 2774460, "relation_to_type": "type", "validated": true, "ani": 88.2392, "matched_fragments": 1694, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas bananamidigenes", "strain": "strain=BW11P2", "accession": "GCA_001679645.1", "taxid": 2843610, "species_taxid": 2843610, "relation_to_type": "type", "validated": true, "ani": 87.7979, "matched_fragments": 1584, "total_fragments": 2041, "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": 86.4348, "matched_fragments": 1498, "total_fragments": 2041, "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": 86.3382, "matched_fragments": 1413, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas granadensis", "strain": "strain=LMG 27940", "accession": "GCA_900105485.1", "taxid": 1421430, "species_taxid": 1421430, "relation_to_type": "suspected-type", "validated": true, "ani": 86.2374, "matched_fragments": 1549, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas germanica", "strain": "strain=FIT28", "accession": "GCA_019614655.1", "taxid": 2815720, "species_taxid": 2815720, "relation_to_type": "type", "validated": true, "ani": 86.1915, "matched_fragments": 1625, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas crudilactis", "strain": "strain=UCMA 17988", "accession": "GCA_013433315.1", "taxid": 2697028, "species_taxid": 2697028, "relation_to_type": "type", "validated": true, "ani": 86.1018, "matched_fragments": 1612, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=LMG 1245", "accession": "GCA_001269575.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 85.8781, "matched_fragments": 1493, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=NBRC 3521", "accession": "GCA_000813225.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 85.8752, "matched_fragments": 1481, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azerbaijanoriens", "strain": "strain=SWRI123", "accession": "GCA_019139795.1", "taxid": 2842350, "species_taxid": 2842350, "relation_to_type": "type", "validated": true, "ani": 85.8736, "matched_fragments": 1429, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurylsulfatiphila", "strain": "strain=AP3_16", "accession": "GCA_002934665.1", "taxid": 2011015, "species_taxid": 2011015, "relation_to_type": "type", "validated": true, "ani": 85.8601, "matched_fragments": 1444, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=CCUG 712", "accession": "GCA_008801625.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 85.8377, "matched_fragments": 1491, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aureofaciens", "strain": "strain=DSM 6698", "accession": "GCA_003851905.1", "taxid": 587851, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 85.7674, "matched_fragments": 1514, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jessenii", "strain": "strain=DSM 17150", "accession": "GCA_002236115.1", "taxid": 77298, "species_taxid": 77298, "relation_to_type": "suspected-type", "validated": true, "ani": 85.7164, "matched_fragments": 1455, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurylsulfativorans", "strain": "strain=AP3_22", "accession": "GCA_002906155.1", "taxid": 1943631, "species_taxid": 1943631, "relation_to_type": "type", "validated": true, "ani": 85.4909, "matched_fragments": 1437, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas thivervalensis", "strain": "strain=DSM 13194", "accession": "GCA_001269655.1", "taxid": 86265, "species_taxid": 86265, "relation_to_type": "type", "validated": true, "ani": 85.1502, "matched_fragments": 1325, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas umsongensis", "strain": "strain=DSM 16611", "accession": "GCA_002236105.1", "taxid": 198618, "species_taxid": 198618, "relation_to_type": "type", "validated": true, "ani": 85.1192, "matched_fragments": 1358, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lurida", "strain": "strain=LMG 21995", "accession": "GCA_002563895.1", "taxid": 244566, "species_taxid": 244566, "relation_to_type": "type", "validated": true, "ani": 83.6951, "matched_fragments": 1299, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicae", "strain": "strain=MAFF 212427", "accession": "GCA_010671725.1", "taxid": 2708063, "species_taxid": 2708063, "relation_to_type": "type", "validated": true, "ani": 83.4899, "matched_fragments": 924, "total_fragments": 2041, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002113595.1", "gtdb_species": "s__Pseudomonas_E sp002113595", "ani": 96.4195, "matched_fragments": 1889, "total_fragments": 2041, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "96.42", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 16, "status": "conclusive" }, { "accession": "GCF_004006335.1", "gtdb_species": "s__Pseudomonas_E sp002112885", "ani": 88.4761, "matched_fragments": 1672, "total_fragments": 2041, "gtdb_taxonomy": 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