{ "type": "genome", "identifier": "GCF_016937615.1", "organism": "Pseudomonas lactucae", "title": "Pseudomonas lactucae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Agriculture and Food Research Organization (NARO)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016937615.1", "bioproject": "PRJNA224116", "biosample": "SAMN17975957", "wgs_master": "JAFHKI000000000.1", "refseq_category": "na", "taxid": "2813360", "species_taxid": "2813360", "organism_name": "Pseudomonas lactucae", "infraspecific_name": "strain=MAFF 301380", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/24", "asm_name": "ASM1693761v1", "asm_submitter": "National Agriculture and Food Research Organization (NARO)", "gbrs_paired_asm": "GCA_016937615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/937/615/GCF_016937615.1_ASM1693761v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6257033", "genome_size_ungapped": "6257033", "gc_percent": "60.500000", "replicon_count": "0", "scaffold_count": "268", "contig_count": "268", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016937615.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "5897", "protein_coding_gene_count": "5159", "non_coding_gene_count": "68", "pubmed_id": "34309505" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-24", "dateModified": "2021-02-24", "datePublished": "2021-02-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas lactucae" ], "sample_taxid": [ "2813360" ], "sample_host_organism": [ "lettuce" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Tokushima" ], "sample_host_location_id": [], "data_size": "1.769 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)": "6257033", "Number of Sequences": "268", "Longest Sequences (bp)": "179475", "N50 (bp)": "45859", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.4", "Number of CDSs": "6114", "Average Protein Length": "298.5", "Coding Ratio (%)": "87.5", "Number of rRNAs": "5", "Number of tRNAs": "61", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas lactucae", "strain": "strain=MAFF 301380", "accession": "GCA_016937615.1", "taxid": 2813360, "species_taxid": 2813360, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1942, "total_fragments": 1959, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas asgharzadehiana", "strain": "strain=SWRI132", "accession": "GCA_019139815.1", "taxid": 2842349, "species_taxid": 2842349, "relation_to_type": "type", "validated": true, "ani": 90.7652, "matched_fragments": 1548, "total_fragments": 1959, "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": 88.9866, "matched_fragments": 1553, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azotoformans", "strain": "strain=NBRC 12693", "accession": "GCA_002091515.1", "taxid": 47878, "species_taxid": 47878, "relation_to_type": "suspected-type", 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1486, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas marginalis", "strain": "strain=ICMP 3553", "accession": "GCA_003700725.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 88.367, "matched_fragments": 1403, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas simiae", "strain": "strain=CCUG 50988", "accession": "GCA_001730615.1", "taxid": 321846, "species_taxid": 321846, "relation_to_type": "type", "validated": true, "ani": 88.1299, "matched_fragments": 1427, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas simiae", "strain": "strain=CCUG 50988", "accession": "GCA_900111895.1", "taxid": 321846, "species_taxid": 321846, "relation_to_type": "type", "validated": true, "ani": 88.1029, "matched_fragments": 1424, "total_fragments": 1959, "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": 88.082, "matched_fragments": 1415, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas extremaustralis", "strain": "strain=DSM 17835", "accession": "GCA_007858235.1", "taxid": 359110, "species_taxid": 359110, "relation_to_type": "type", "validated": true, "ani": 88.0658, "matched_fragments": 1385, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lactis", "strain": "strain=DSM 29167", "accession": "GCA_001439845.1", "taxid": 1615674, "species_taxid": 1615674, "relation_to_type": "type", "validated": true, "ani": 87.6987, "matched_fragments": 1429, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas salmasensis", "strain": "strain=SWRI126", "accession": "GCA_014268375.2", "taxid": 2745514, "species_taxid": 2745514, "relation_to_type": "type", "validated": true, "ani": 87.655, "matched_fragments": 1421, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas paracarnis", "strain": "strain=V5/DAB/2/5", "accession": "GCA_904063055.1", "taxid": 2750625, "species_taxid": 2750625, "relation_to_type": "type", "validated": true, "ani": 87.6301, "matched_fragments": 1403, "total_fragments": 1959, "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": 87.6163, "matched_fragments": 1394, "total_fragments": 1959, "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": 87.573, "matched_fragments": 1406, "total_fragments": 1959, "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": 87.5077, "matched_fragments": 1423, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas paralactis", "strain": "strain=DSM 29164", "accession": "GCA_001439735.1", "taxid": 1615673, "species_taxid": 1615673, "relation_to_type": "type", "validated": true, "ani": 87.4015, "matched_fragments": 1373, "total_fragments": 1959, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas spelaei", "strain": "strain=CCM 7893", "accession": 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