{ "type": "genome", "identifier": "GCF_003586265.1", "organism": "Pseudomonas jilinensis", "title": "Pseudomonas jilinensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Peking university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003586265.1", "bioproject": "PRJNA224116", "biosample": "SAMN08389690", "wgs_master": "QJSA00000000.1", "refseq_category": "reference genome", "taxid": "2078689", "species_taxid": "2078689", "organism_name": "Pseudomonas jilinensis", "infraspecific_name": "strain=JS15-10A1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/09/10", "asm_name": "ASM358626v1", "asm_submitter": "Peking university", "gbrs_paired_asm": "GCA_003586265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/586/265/GCF_003586265.1_ASM358626v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3989683", "genome_size_ungapped": "3989683", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "57", "contig_count": "57", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003586265.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3689", "protein_coding_gene_count": "3580", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-09-10", "dateModified": "2018-09-10", "datePublished": "2018-09-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas jilinensis" ], "sample_taxid": [ "2078689" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Jilin oilfield", "Peking university" ], "sample_host_location_id": [], "data_size": "1.121 MB", "sample_ph_range": { "min": 78.0, "max": 78.0 }, "sample_temperature_range": { "min": 20.0, "max": 25.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3989683", "Number of Sequences": "57", "Longest Sequences (bp)": "427024", "N50 (bp)": "220121", "Gap Ratio (%)": "0.000677", "GCcontent (%)": "60.1", "Number of CDSs": "3641", "Average Protein Length": "331.4", "Coding Ratio (%)": "90.7", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas yangmingensis", "strain": "strain=DSM 24213", "accession": "GCA_900114825.1", "taxid": 1720063, "species_taxid": 1720063, "relation_to_type": "type", "validated": true, "ani": 80.235, "matched_fragments": 525, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas pachastrellae", "strain": "strain=CCUG 46540", "accession": "GCA_001989375.1", "taxid": 254161, "species_taxid": 254161, "relation_to_type": "type", "validated": true, "ani": 79.9539, "matched_fragments": 531, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas pachastrellae", "strain": "strain=JCM 12285", "accession": "GCA_900114765.1", "taxid": 254161, "species_taxid": 254161, "relation_to_type": "type", "validated": true, "ani": 79.9465, "matched_fragments": 548, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas aestusnigri", "strain": "strain=CECT 8317", "accession": "GCA_900108005.1", "taxid": 857252, "species_taxid": 857252, "relation_to_type": "type", "validated": true, "ani": 79.7781, "matched_fragments": 549, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas aestusnigri", "strain": "strain=VGXO14", "accession": "GCA_002197985.1", "taxid": 857252, "species_taxid": 857252, "relation_to_type": "type", "validated": true, "ani": 79.7419, "matched_fragments": 547, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas bauzanensis", "strain": "strain=CGMCC 1.9095", "accession": "GCA_900114735.1", "taxid": 653930, "species_taxid": 653930, "relation_to_type": "type", "validated": true, "ani": 79.6193, "matched_fragments": 476, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas bauzanensis", "strain": "strain=DSM 22558", "accession": "GCA_900111225.1", "taxid": 653930, "species_taxid": 653930, "relation_to_type": "type", "validated": true, "ani": 79.5718, "matched_fragments": 484, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 79.3235, "matched_fragments": 459, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas litoralis", "strain": "strain=2SM5", "accession": "GCA_900105005.1", "taxid": 797277, "species_taxid": 797277, "relation_to_type": "type", "validated": true, "ani": 79.0881, "matched_fragments": 445, "total_fragments": 1305, "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": 78.9176, "matched_fragments": 434, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas profundi", "strain": "strain=M5", "accession": "GCA_008638305.1", "taxid": 1981513, "species_taxid": 1981513, "relation_to_type": "type", "validated": true, "ani": 78.6541, "matched_fragments": 393, "total_fragments": 1305, "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": 78.6335, "matched_fragments": 368, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azotobacter chroococcum subsp. isscasi", "strain": "strain=P205", "accession": "GCA_004327895.1", "taxid": 2528971, "species_taxid": 353, "relation_to_type": "type", "validated": true, "ani": 78.5587, "matched_fragments": 329, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas saliphila", "strain": "strain=16W4-4-3", "accession": "GCA_008638345.1", "taxid": 2586906, "species_taxid": 2586906, "relation_to_type": "type", "validated": true, "ani": 78.5048, "matched_fragments": 387, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas thermotolerans", "strain": "strain=DSM 14292", "accession": "GCA_000364625.1", "taxid": 157784, "species_taxid": 157784, "relation_to_type": "type", "validated": true, "ani": 78.3807, "matched_fragments": 355, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=NCTC10332", "accession": "GCA_001457615.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 78.3746, "matched_fragments": 395, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_012987025.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 78.3568, "matched_fragments": 394, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_001042925.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 78.3568, "matched_fragments": 394, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas chloritidismutans", "strain": "strain=AW-1", "accession": "GCA_000495915.1", "taxid": 203192, "species_taxid": 203192, "relation_to_type": "type", "validated": true, "ani": 78.3164, "matched_fragments": 353, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aeruginosa", "strain": "strain=DSM 50071", "accession": "GCA_900167195.1", "taxid": 287, "species_taxid": 287, "relation_to_type": "type", "validated": true, "ani": 78.2789, "matched_fragments": 403, "total_fragments": 1305, "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": 78.239, "matched_fragments": 320, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_021602585.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 78.211, "matched_fragments": 334, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella variicola", "strain": "strain=DSM 15968", "accession": "GCA_000828055.2", "taxid": 244366, "species_taxid": 244366, "relation_to_type": "type", "validated": true, "ani": 75.8534, "matched_fragments": 62, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella variicola subsp. variicola", "strain": "strain=F2R9T", "accession": "GCA_020525545.1", "taxid": 2590157, "species_taxid": 244366, "relation_to_type": "type", "validated": true, "ani": 75.8534, "matched_fragments": 62, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella variicola", "strain": "strain=F2R9", "accession": "GCA_017638945.1", "taxid": 244366, "species_taxid": 244366, "relation_to_type": "type", "validated": true, "ani": 75.8534, "matched_fragments": 62, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella variicola", "strain": "strain=type strain: F2R9", "accession": "GCA_900978195.1", "taxid": 244366, "species_taxid": 244366, "relation_to_type": "type", "validated": true, "ani": 75.568, "matched_fragments": 60, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003586265.1", "gtdb_species": "s__Pseudomonas_D jilinensis", "ani": 100.0, "matched_fragments": 1303, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.07", "min_intra_species_ani": "95.47", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_900114825.1", "gtdb_species": "s__Pseudomonas_D yangmingensis", "ani": 80.2052, "matched_fragments": 527, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": 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"min_intra_species_af": "0.72", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_002979975.1", "gtdb_species": "s__Pseudomonas_D sp002979975", "ani": 79.8638, "matched_fragments": 550, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_900115905.1", "gtdb_species": "s__Pseudomonas_D formosensis", "ani": 79.8241, "matched_fragments": 512, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000939975.1", "gtdb_species": "s__Pseudomonas_D saudimassiliensis", "ani": 79.7994, "matched_fragments": 479, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002197985.1", "gtdb_species": "s__Pseudomonas_D aestusnigri", "ani": 79.7565, "matched_fragments": 545, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "96.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_900114735.1", "gtdb_species": "s__Pseudomonas_D bauzanensis", "ani": 79.6192, "matched_fragments": 476, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_019116555.1", "gtdb_species": "s__Pseudomonas_D excrementavium", "ani": 79.5114, "matched_fragments": 398, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_014646575.1", "gtdb_species": "s__Pseudomonas_D pertucinogena", "ani": 79.2854, "matched_fragments": 445, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_002091635.1", "gtdb_species": "s__Pseudomonas_M indica", "ani": 79.0984, "matched_fragments": 372, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.16", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900105005.1", "gtdb_species": "s__Pseudomonas_D litoralis", "ani": 79.0896, "matched_fragments": 448, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_002296055.1", "gtdb_species": "s__Pseudomonas_D sp002296055", "ani": 79.0698, "matched_fragments": 435, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_900105655.1", "gtdb_species": "s__Pseudomonas_D salegens", "ani": 79.0648, "matched_fragments": 451, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_009497895.1", "gtdb_species": "s__Pseudomonas_D pelagia_A", "ani": 79.018, "matched_fragments": 497, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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, 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"accession": "GCF_000495915.1", "gtdb_species": "s__Pseudomonas_A chloritidismutans", "ani": 78.3108, "matched_fragments": 355, "total_fragments": 1305, "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_000802155.2", "gtdb_species": "s__Pseudomonas_E frederiksbergensis_A", "ani": 77.7488, "matched_fragments": 299, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.21", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" } 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