{ "type": "genome", "identifier": "GCF_005863185.1", "organism": "Pseudomonas edaphica", "title": "Pseudomonas edaphica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005863185.1", "bioproject": "PRJNA224116", "biosample": "SAMN11651189", "wgs_master": "VBVZ00000000.1", "refseq_category": "na", "taxid": "2006980", "species_taxid": "2006980", "organism_name": "Pseudomonas edaphica", "infraspecific_name": "strain=RD25", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/22", "asm_name": "ASM586318v1", "asm_submitter": "CSIC", "gbrs_paired_asm": "GCA_005863185.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/863/185/GCF_005863185.1_ASM586318v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6734981", "genome_size_ungapped": "6734981", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "1154", "contig_count": "1154", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005863185.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "6702", "protein_coding_gene_count": "6261", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-05-22", "dateModified": "2019-05-22", "datePublished": "2019-05-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas edaphica" ], "sample_taxid": [ "2006980" ], "sample_host_organism": [ "rhizospheric soil of Cistus ladanifer L." ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain: Rabanales (Zamora)" ], "sample_host_location_id": [], "data_size": "1.919 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.46, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "6734981", "Number of Sequences": "1154", "Longest Sequences (bp)": "43009", "N50 (bp)": "9419", "Gap Ratio (%)": "0.000015", "GCcontent (%)": "59.9", "Number of CDSs": "5419", "Average Protein Length": "303.4", "Coding Ratio (%)": "73.2", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas edaphica", "strain": "strain=RD25", "accession": "GCA_005863185.1", "taxid": 2006980, "species_taxid": 2006980, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1666, "total_fragments": 1694, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas salomonii", "strain": "strain=LMG 22120", "accession": "GCA_001730645.1", "taxid": 191391, "species_taxid": 191391, "relation_to_type": "type", "validated": true, "ani": 94.6009, "matched_fragments": 1424, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas salomonii", "strain": "strain=ICMP 14252", "accession": "GCA_900107155.1", "taxid": 191391, "species_taxid": 191391, "relation_to_type": "type", "validated": true, "ani": 94.5378, "matched_fragments": 1443, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=DSM 50090", "accession": "GCA_007858165.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 89.3161, "matched_fragments": 1370, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=NBRC 14160", "accession": "GCA_002091595.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 89.2975, "matched_fragments": 1362, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fluorescens", "strain": "strain=NCTC10038", "accession": "GCA_900475215.1", "taxid": 294, "species_taxid": 294, "relation_to_type": "suspected-type", "validated": true, "ani": 89.2731, "matched_fragments": 1373, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas marginalis", "strain": "strain=DSM 13124", "accession": "GCA_007858155.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 88.1117, "matched_fragments": 1257, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, "relation_to_type": "type", "validated": true, "ani": 88.017, "matched_fragments": 1285, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lurida", "strain": "strain=LMG 21995", "accession": "GCA_002563895.1", "taxid": 244566, "species_taxid": 244566, "relation_to_type": "type", "validated": true, "ani": 87.7486, "matched_fragments": 1269, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas asgharzadehiana", "strain": "strain=SWRI132", "accession": "GCA_019139815.1", "taxid": 2842349, "species_taxid": 2842349, "relation_to_type": "type", "validated": true, "ani": 87.537, "matched_fragments": 1194, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas yamanorum", "strain": "strain=LMG 27247", "accession": "GCA_900105735.1", "taxid": 515393, "species_taxid": 515393, "relation_to_type": "suspected-type", "validated": true, "ani": 86.8451, "matched_fragments": 1294, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas proteolytica", "strain": "strain=DSM 15321", "accession": "GCA_007858275.1", "taxid": 219574, "species_taxid": 219574, "relation_to_type": "type", "validated": true, "ani": 86.0492, "matched_fragments": 1135, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas spelaei", "strain": "strain=CCM 7893", "accession": "GCA_009724245.1", "taxid": 1055469, "species_taxid": 1055469, "relation_to_type": "type", "validated": true, "ani": 85.9029, "matched_fragments": 1217, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas karstica", "strain": "strain=CCM 7891", "accession": "GCA_009707515.1", "taxid": 1055468, "species_taxid": 1055468, 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79.7868, "matched_fragments": 543, "total_fragments": 1694, "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": 79.752, "matched_fragments": 575, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Malikia granosa", "strain": "strain=P1", "accession": "GCA_002980595.1", "taxid": 263067, "species_taxid": 263067, "relation_to_type": "type", "validated": true, "ani": 75.7808, "matched_fragments": 87, "total_fragments": 1694, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arenimonas composti", "strain": "strain=TR7-09", "accession": "GCA_000747175.1", "taxid": 370776, "species_taxid": 370776, "relation_to_type": "type", "validated": true, "ani": 75.7496, "matched_fragments": 86, "total_fragments": 1694, "ani_threshold": 95, 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