{ "type": "genome", "identifier": "GCF_003052605.1", "organism": "Pseudomonas indoloxydans", "title": "Pseudomonas indoloxydans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003052605.1", "bioproject": "PRJNA224116", "biosample": "SAMN08891239", "wgs_master": "QASO00000000.1", "refseq_category": "reference genome", "taxid": "404407", "species_taxid": "404407", "organism_name": "Pseudomonas indoloxydans", "infraspecific_name": "strain=JCM 14246", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/17", "asm_name": "ASM305260v1", "asm_submitter": "Zhejiang university", "gbrs_paired_asm": "GCA_003052605.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/052/605/GCF_003052605.1_ASM305260v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5199651", "genome_size_ungapped": "5198591", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "143", "contig_count": "143", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003052605.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "5134", "protein_coding_gene_count": "4772", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-17", "dateModified": "2018-04-17", "datePublished": "2018-04-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas indoloxydans" ], "sample_taxid": [ "404407" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.457 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)": "5199651", "Number of Sequences": "143", "Longest Sequences (bp)": "212576", "N50 (bp)": "60031", "Gap Ratio (%)": "0.020636", "GCcontent (%)": "62.2", "Number of CDSs": "5006", "Average Protein Length": "299.5", "Coding Ratio (%)": "86.5", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 96.4045, "matched_fragments": 1250, "total_fragments": 1662, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas oleovorans subsp. oleovorans", "strain": "strain=DSM 1045", "accession": "GCA_002197815.1", "taxid": 1218129, "species_taxid": 301, "relation_to_type": "type", "validated": true, "ani": 96.4011, "matched_fragments": 1252, "total_fragments": 1662, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas oleovorans", "strain": "strain=NCTC10692", "accession": "GCA_900455615.1", "taxid": 301, "species_taxid": 301, "relation_to_type": "type", "validated": true, "ani": 96.3699, "matched_fragments": 1282, "total_fragments": 1662, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=DSM 26382", "accession": "GCA_012986985.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 93.647, "matched_fragments": 1218, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=MBR", "accession": "GCA_017905455.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 93.5994, "matched_fragments": 1217, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chengduensis", "strain": "strain=DSM 26382", "accession": "GCA_900102635.1", "taxid": 489632, "species_taxid": 489632, "relation_to_type": "type", "validated": true, "ani": 93.5948, "matched_fragments": 1230, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas toyotomiensis", "strain": "strain=DSM 26169", "accession": "GCA_002741095.1", "taxid": 554344, "species_taxid": 554344, "relation_to_type": "type", "validated": true, "ani": 92.6269, "matched_fragments": 1212, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas toyotomiensis", "strain": "strain=JCM 15604", "accession": "GCA_900115695.1", "taxid": 554344, "species_taxid": 554344, "relation_to_type": "type", "validated": true, "ani": 92.5607, "matched_fragments": 1209, "total_fragments": 1662, "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": 90.9035, "matched_fragments": 1147, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaliphila", "strain": "strain=JCM 10630", "accession": "GCA_900101755.1", "taxid": 101564, "species_taxid": 101564, "relation_to_type": "type", "validated": true, "ani": 90.748, "matched_fragments": 1180, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas alcaliphila", "strain": "strain=NBRC 102411", "accession": "GCA_002091495.1", "taxid": 101564, "species_taxid": 101564, "relation_to_type": "type", "validated": true, "ani": 90.7417, "matched_fragments": 1178, "total_fragments": 1662, "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": 89.2864, "matched_fragments": 1184, "total_fragments": 1662, "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": 88.8063, "matched_fragments": 1131, "total_fragments": 1662, "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": 88.3219, "matched_fragments": 1158, "total_fragments": 1662, "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": 82.1929, "matched_fragments": 834, "total_fragments": 1662, "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": 82.1466, "matched_fragments": 791, "total_fragments": 1662, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003052605.1", "gtdb_species": "s__Pseudomonas_E indoloxydans", "ani": 100.0, "matched_fragments": 1642, "total_fragments": 1662, "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": "conclusive" }, { "accession": "GCF_002197815.1", "gtdb_species": "s__Pseudomonas_E oleovorans", "ani": 96.4072, "matched_fragments": 1252, "total_fragments": 1662, "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_001941865.1", "gtdb_species": "s__Pseudomonas_E alcaliphila_B", "ani": 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93.5827, "matched_fragments": 1227, "total_fragments": 1662, "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": "-" }, { "accession": "GCF_002803095.1", "gtdb_species": "s__Pseudomonas_E sp002803095", "ani": 92.953, "matched_fragments": 1212, "total_fragments": 1662, "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": 92.5458, 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