{ "type": "genome", "identifier": "GCF_013373895.1", "organism": "Pseudomonas ceruminis", "title": "Pseudomonas ceruminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Juntendo University School of Medicine Department of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013373895.1", "bioproject": "PRJNA224116", "biosample": "SAMD00229128", "wgs_master": "BLXP00000000.1", "refseq_category": "na", "taxid": "2740516", "species_taxid": "2740516", "organism_name": "Pseudomonas ceruminis", "infraspecific_name": "strain=BML-PP028", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/11", "asm_name": "ASM1337389v1", "asm_submitter": "Juntendo University School of Medicine Department of Microbiology", "gbrs_paired_asm": "GCA_013373895.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/373/895/GCF_013373895.1_ASM1337389v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6351217", "genome_size_ungapped": "6351217", "gc_percent": "61.500000", "replicon_count": "0", "scaffold_count": "283", "contig_count": "283", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013373895.1-RS_2024_08_02", "annotation_date": "2024-08-02", "total_gene_count": "6127", "protein_coding_gene_count": "5857", "non_coding_gene_count": "83", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-11", "dateModified": "2020-06-11", "datePublished": "2020-06-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas ceruminis" ], "sample_taxid": [ "2740516" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Tokyo" ], "sample_host_location_id": [], "data_size": "1.786 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6346751", "Number of Sequences": "252", "Longest Sequences (bp)": "396795", "N50 (bp)": "135871", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "61.7", "Number of CDSs": "5866", "Average Protein Length": "314.4", "Coding Ratio (%)": "87.2", "Number of rRNAs": "5", "Number of tRNAs": "71", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas ceruminis", "strain": "strain=BML-PP028", "accession": "GCA_013373895.1", "taxid": 2740516, "species_taxid": 2740516, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2037, "total_fragments": 2042, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas ceruminis", "strain": "strain=BML-PP028", "accession": "GCA_021602025.1", "taxid": 2740516, "species_taxid": 2740516, "relation_to_type": "type", "validated": true, "ani": 99.9983, "matched_fragments": 2038, "total_fragments": 2042, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_021602585.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 88.2645, "matched_fragments": 1397, "total_fragments": 2042, "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": 88.2561, "matched_fragments": 1309, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas plecoglossicida", "strain": "strain=NBRC 103162", "accession": "GCA_000730665.1", "taxid": 70775, "species_taxid": 70775, "relation_to_type": "suspected-type", "validated": true, "ani": 87.6237, "matched_fragments": 1287, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas plecoglossicida", "strain": "strain=DSM 15088", "accession": "GCA_000688275.1", "taxid": 70775, "species_taxid": 70775, "relation_to_type": "suspected-type", "validated": true, "ani": 87.5947, "matched_fragments": 1312, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_013373915.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 87.0676, "matched_fragments": 1344, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas urethralis", "strain": "strain=BML-PP042", "accession": "GCA_021602465.1", "taxid": 2740517, "species_taxid": 2740517, "relation_to_type": "suspected-type", "validated": true, "ani": 87.0521, "matched_fragments": 1377, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_022548835.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 86.8054, "matched_fragments": 1245, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_000731675.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 86.7851, "matched_fragments": 1363, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas anuradhapurensis", "strain": "strain=RD8MR3", "accession": "GCA_014269225.2", "taxid": 485870, "species_taxid": 485870, "relation_to_type": "type", "validated": true, "ani": 86.633, "matched_fragments": 1272, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kermanshahensis", "strain": "strain=SWRI100", "accession": "GCA_014269205.2", "taxid": 2745482, "species_taxid": 2745482, "relation_to_type": "type", "validated": true, "ani": 86.5306, "matched_fragments": 1351, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oryzicola", "strain": "strain=RD9SR1", "accession": "GCA_014269185.2", "taxid": 485876, "species_taxid": 485876, "relation_to_type": "type", "validated": true, "ani": 86.3771, "matched_fragments": 1279, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas muyukensis", "strain": "strain=COW39", "accession": "GCA_019139535.1", "taxid": 2842357, "species_taxid": 2842357, "relation_to_type": "type", "validated": true, "ani": 85.9383, "matched_fragments": 1253, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas defluvii", "strain": "strain=WCHP16", "accession": "GCA_001695625.1", "taxid": 1876757, "species_taxid": 1876757, "relation_to_type": "type", "validated": true, "ani": 82.1526, "matched_fragments": 832, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=RLD-1", "accession": "GCA_900187975.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 80.7624, "matched_fragments": 905, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=CCM 7361", "accession": "GCA_900099945.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 80.7429, "matched_fragments": 893, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizoryzae", "strain": "strain=RY24", "accession": "GCA_005250615.1", "taxid": 2571129, "species_taxid": 2571129, "relation_to_type": "type", "validated": true, "ani": 79.1717, "matched_fragments": 540, "total_fragments": 2042, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001320525.1", "gtdb_species": "s__Pseudomonas_E sp001320525", "ani": 98.7757, "matched_fragments": 1777, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "98.78", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 10, "status": "conclusive" }, { "accession": "GCF_013373935.1", "gtdb_species": "s__Pseudomonas_E sp002438125", "ani": 88.2772, "matched_fragments": 1307, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.14", "min_intra_species_ani": "98.14", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000282535.1", "gtdb_species": "s__Pseudomonas_E sp000282535", "ani": 87.7656, "matched_fragments": 1247, "total_fragments": 2042, "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_000730665.1", "gtdb_species": "s__Pseudomonas_E plecoglossicida", "ani": 87.6338, "matched_fragments": 1286, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.81", "min_intra_species_ani": "99.74", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002112505.1", "gtdb_species": "s__Pseudomonas_E sp002112505", "ani": 87.5578, "matched_fragments": 1400, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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": "0.99", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_003428805.1", "gtdb_species": "s__Pseudomonas_E sp003428805", "ani": 87.4844, "matched_fragments": 1467, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.29", "min_intra_species_ani": "96.05", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000019445.1", "gtdb_species": "s__Pseudomonas_E putida_E", "ani": 87.4571, "matched_fragments": 1383, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.71", "min_intra_species_ani": "96.19", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_000935045.1", "gtdb_species": "s__Pseudomonas_E sp000935045", "ani": 87.0436, "matched_fragments": 1345, "total_fragments": 2042, "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_002165135.1", "gtdb_species": "s__Pseudomonas_E sp002165135", "ani": 86.7857, "matched_fragments": 1274, "total_fragments": 2042, "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_000731675.1", "gtdb_species": "s__Pseudomonas_E capeferrum", "ani": 86.7778, "matched_fragments": 1364, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002736125.1", "gtdb_species": "s__Pseudomonas_E putida_M", "ani": 86.6298, "matched_fragments": 1374, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.41", "min_intra_species_ani": "97.25", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_000730605.1", "gtdb_species": "s__Pseudomonas_E monteilii", "ani": 86.4725, "matched_fragments": 1381, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.79", "num_clustered_genomes": 45, "status": "-" }, { "accession": "GCF_016648105.1", "gtdb_species": "s__Pseudomonas_E sp016648105", "ani": 86.4017, "matched_fragments": 1249, "total_fragments": 2042, "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_002356095.1", "gtdb_species": "s__Pseudomonas_E putida_H", "ani": 86.1421, "matched_fragments": 1475, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "98.35", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.82", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_003671955.1", "gtdb_species": "s__Pseudomonas_E hunanensis", "ani": 85.9941, "matched_fragments": 1312, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.33", "min_intra_species_ani": "95.26", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.79", "num_clustered_genomes": 88, "status": "-" }, { "accession": "GCF_019139535.1", "gtdb_species": "s__Pseudomonas_E sp019139535", "ani": 85.9519, "matched_fragments": 1252, "total_fragments": 2042, "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_004519305.1", "gtdb_species": "s__Pseudomonas_E sp004519305", "ani": 85.8089, "matched_fragments": 1193, "total_fragments": 2042, "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_009932375.1", "gtdb_species": "s__Pseudomonas_E juntendi", "ani": 85.7585, "matched_fragments": 1201, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.06", "min_intra_species_ani": "97.13", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.79", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_002741075.1", "gtdb_species": "s__Pseudomonas_E putida_T", "ani": 85.4266, "matched_fragments": 1244, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "95.06", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_004357765.1", "gtdb_species": "s__Pseudomonas_E putida_U", "ani": 85.3386, "matched_fragments": 1211, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.43", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013523055.1", "gtdb_species": "s__Pseudomonas_E capeferrum_A", "ani": 83.2703, "matched_fragments": 1111, "total_fragments": 2042, "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_002806685.1", "gtdb_species": "s__Pseudomonas_E qingdaonensis", "ani": 83.246, "matched_fragments": 1156, "total_fragments": 2042, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.05", "min_intra_species_ani": "98.91", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 13, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.767, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 5663774.24, "gc_content": 60.938, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "range_salinity": 0.666, "facultative_respiration": 0.021, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.978, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 0.988, "coccus_cell_shape": 0.011, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "ceruminis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }