{ "type": "genome", "identifier": "GCF_900102635.1", "organism": "Ectopseudomonas chengduensis", "title": "Ectopseudomonas chengduensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900102635.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216576", "wgs_master": "FMZQ00000000.1", "refseq_category": "na", "taxid": "489632", "species_taxid": "489632", "organism_name": "Ectopseudomonas chengduensis", "infraspecific_name": "strain=DSM 26382", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/21", "asm_name": "IMG-taxon 2663762777 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900102635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/102/635/GCF_900102635.1_IMG-taxon_2663762777_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5413065", "genome_size_ungapped": "5412239", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900102635.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "5197", "protein_coding_gene_count": "5056", "non_coding_gene_count": "74", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-21", "dateModified": "2016-10-21", "datePublished": "2016-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Ectopseudomonas chengduensis" ], "sample_taxid": [ "489632" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.506 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)": "5413065", "Number of Sequences": "43", "Longest Sequences (bp)": "1013045", "N50 (bp)": "248272", "Gap Ratio (%)": "0.015259", "GCcontent (%)": "62.3", "Number of CDSs": "5143", "Average Protein Length": "312.5", "Coding Ratio (%)": "89.1", "Number of rRNAs": "3", "Number of tRNAs": "68", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas chengduensis", "strain": "strain=DSM 26382", "accession": "GCA_900102635.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1781, "total_fragments": 1782, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=DSM 26382", "accession": "GCA_012986985.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 99.9923, "matched_fragments": 1772, "total_fragments": 1782, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=MBR", "accession": "GCA_017905455.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 99.9878, "matched_fragments": 1755, "total_fragments": 1782, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas sihuiensis", "strain": "strain=KCTC 32246", "accession": "GCA_900106015.1", "taxid": 1274359, "species_taxid": 1274359, "relation_to_type": "type", "validated": true, "ani": 96.7402, "matched_fragments": 1519, "total_fragments": 1782, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas toyotomiensis", "strain": "strain=DSM 26169", "accession": "GCA_002741095.1", "taxid": 554344, "species_taxid": 554344, "relation_to_type": "type", "validated": true, "ani": 95.0318, "matched_fragments": 1485, "total_fragments": 1782, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas toyotomiensis", "strain": "strain=JCM 15604", "accession": "GCA_900115695.1", "taxid": 554344, "species_taxid": 554344, "relation_to_type": "type", "validated": true, "ani": 94.9765, "matched_fragments": 1501, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas oleovorans subsp. oleovorans", "strain": "strain=NBRC 13583", "accession": "GCA_002091815.1", "taxid": 1218129, "species_taxid": 301, "relation_to_type": "type", "validated": true, "ani": 93.6106, "matched_fragments": 1193, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sediminis", "strain": "strain=PI11", "accession": "GCA_002741105.1", "taxid": 1691904, "species_taxid": 1691904, "relation_to_type": "type", "validated": true, "ani": 91.7288, "matched_fragments": 1423, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas guguanensis", "strain": "strain=JCM 18416", "accession": "GCA_900104265.1", "taxid": 1198456, "species_taxid": 1198456, "relation_to_type": "type", "validated": true, "ani": 89.8301, "matched_fragments": 1363, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas yangonensis", "strain": "strain=MY50", "accession": "GCA_009932725.1", "taxid": 2579922, "species_taxid": 2579922, "relation_to_type": "type", "validated": true, "ani": 89.2599, "matched_fragments": 1308, "total_fragments": 1782, "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": 89.2152, "matched_fragments": 1337, "total_fragments": 1782, "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": 82.3202, "matched_fragments": 909, "total_fragments": 1782, "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": 82.1639, "matched_fragments": 912, "total_fragments": 1782, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900102635.1", "gtdb_species": "s__Pseudomonas_E chengduensis", "ani": 100.0, "matched_fragments": 1781, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 96.7402, "mean_intra_species_ani": "99.23", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_900106015.1", "gtdb_species": "s__Pseudomonas_E sihuiensis", "ani": 96.7402, "matched_fragments": 1519, "total_fragments": 1782, "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": "conclusive" }, { "accession": "GCF_015712065.1", "gtdb_species": "s__Pseudomonas_E chengduensis_A", "ani": 96.6919, "matched_fragments": 1531, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 96.7107, "mean_intra_species_ani": "97.25", "min_intra_species_ani": "97.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001941865.1", "gtdb_species": "s__Pseudomonas_E alcaliphila_B", "ani": 95.7316, "matched_fragments": 1455, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.7502, "mean_intra_species_ani": "96.52", "min_intra_species_ani": "96.24", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002803095.1", "gtdb_species": "s__Pseudomonas_E sp002803095", "ani": 95.6316, "matched_fragments": 1472, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.6432, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900115695.1", "gtdb_species": "s__Pseudomonas_E toyotomiensis", "ani": 94.9765, "matched_fragments": 1501, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.1942, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "97.23", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003052605.1", "gtdb_species": "s__Pseudomonas_E indoloxydans", "ani": 93.6667, "matched_fragments": 1217, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 96.52, "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_002197815.1", "gtdb_species": "s__Pseudomonas_E oleovorans", "ani": 93.6083, "matched_fragments": 1202, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 96.52, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "96.68", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.80", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_902506495.1", "gtdb_species": "s__Pseudomonas_E sp902506495", "ani": 92.7454, "matched_fragments": 1451, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "95.94", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002741105.1", "gtdb_species": "s__Pseudomonas_E sediminis", "ani": 91.7369, "matched_fragments": 1422, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.01", "min_intra_species_ani": "95.51", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_007049795.1", "gtdb_species": "s__Pseudomonas_E mendocina_D", "ani": 91.2342, "matched_fragments": 1294, "total_fragments": 1782, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.17", "min_intra_species_ani": "96.47", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 6, "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 }, "_genome_taxon": [ "Ectopseudomonas", "chengduensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }