{ "type": "genome", "identifier": "GCF_008638305.1", "organism": "Pseudomonas profundi", "title": "Pseudomonas profundi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbiology,Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008638305.1", "bioproject": "PRJNA224116", "biosample": "SAMN12645869", "wgs_master": "VTPZ00000000.1", "refseq_category": "reference genome", "taxid": "1981513", "species_taxid": "1981513", "organism_name": "Pseudomonas profundi", "infraspecific_name": "strain=M5", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/23", "asm_name": "ASM863830v1", "asm_submitter": "Institute of Microbiology,Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_008638305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/638/305/GCF_008638305.1_ASM863830v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4212028", "genome_size_ungapped": "4211976", "gc_percent": "58.500000", "replicon_count": "0", "scaffold_count": "56", "contig_count": "56", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008638305.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "3936", "protein_coding_gene_count": "3806", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-23", "dateModified": "2019-09-23", "datePublished": "2019-09-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas profundi" ], "sample_taxid": [ "1981513" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.195 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)": "4212028", "Number of Sequences": "56", "Longest Sequences (bp)": "662940", "N50 (bp)": "278124", "Gap Ratio (%)": "0.001709", "GCcontent (%)": "58.6", "Number of CDSs": "3873", "Average Protein Length": "318.7", "Coding Ratio (%)": "87.9", "Number of rRNAs": "4", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas profundi", "strain": "strain=M5", "accession": "GCA_008638305.1", "taxid": 1981513, "species_taxid": 1981513, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1375, "total_fragments": 1380, "ani_threshold": 95, "status": "conclusive" }, { "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": 85.2792, "matched_fragments": 1068, "total_fragments": 1380, "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": 80.0756, "matched_fragments": 446, "total_fragments": 1380, "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": 79.1354, 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"total_fragments": 1380, "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": 78.5176, "matched_fragments": 368, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas oceani", "strain": "strain=DSM 100277", "accession": "GCA_002903165.1", "taxid": 1708783, "species_taxid": 1708783, "relation_to_type": "type", "validated": true, "ani": 78.443, "matched_fragments": 361, "total_fragments": 1380, "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": 77.4456, "matched_fragments": 215, "total_fragments": 1380, "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": 77.3517, "matched_fragments": 206, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas bharatica", "strain": "strain=CSV86", "accession": "GCA_000319305.2", "taxid": 2692112, "species_taxid": 2692112, "relation_to_type": "type", "validated": true, "ani": 77.2463, "matched_fragments": 216, "total_fragments": 1380, "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": 77.044, "matched_fragments": 211, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas izuensis", "strain": "strain=IzPS43_3003", "accession": "GCA_009861505.1", "taxid": 2684212, "species_taxid": 2684212, "relation_to_type": "type", "validated": true, "ani": 76.8447, "matched_fragments": 194, "total_fragments": 1380, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008638305.1", "gtdb_species": "s__Pseudomonas_D profundi", "ani": 100.0, "matched_fragments": 1375, "total_fragments": 1380, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_012844345.1", "gtdb_species": "s__Pseudomonas_D sp012844345", "ani": 87.5635, "matched_fragments": 1065, "total_fragments": 1380, "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_008638345.1", "gtdb_species": "s__Pseudomonas_D saliphila", "ani": 85.2812, "matched_fragments": 1068, "total_fragments": 1380, "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_900105005.1", "gtdb_species": "s__Pseudomonas_D litoralis", "ani": 80.1155, 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