{ "type": "genome", "identifier": "GCF_028823535.1", "organism": "Pseudomonas serbica", "title": "Pseudomonas serbica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CNRS", "publication": [ {} ], "properties": { "assembly_accession": "GCF_028823535.1", "bioproject": "PRJNA224116", "biosample": "SAMN30035157", "wgs_master": "JAQIYM000000000.1", "refseq_category": "reference genome", "taxid": "2965074", "species_taxid": "2965074", "organism_name": "Pseudomonas serbica", "infraspecific_name": "strain=IT-P366", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/02/23", "asm_name": "ASM2882353v1", "asm_submitter": "CNRS", "gbrs_paired_asm": "GCA_028823535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/028/823/535/GCF_028823535.1_ASM2882353v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7593335", "genome_size_ungapped": "7593335", "gc_percent": "59.500000", "replicon_count": "2", "scaffold_count": "90", "contig_count": "90", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_028823535.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "7329", "protein_coding_gene_count": "7110", "non_coding_gene_count": "115", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-02-23", "dateModified": "2023-02-23", "datePublished": "2023-02-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas serbica" ], "sample_taxid": [ "2965074" ], "sample_host_organism": [ "Triticum aestivum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Serbia" ], "sample_host_location_id": [], "data_size": "2.134 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)": "7593335", "Number of Sequences": "90", "Longest Sequences (bp)": "1059468", "N50 (bp)": "374847", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.5", "Number of CDSs": "7168", "Average Protein Length": "310.1", "Coding Ratio (%)": "87.8", "Number of rRNAs": "1", "Number of tRNAs": "105", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas umsongensis", "strain": "strain=DSM 16611", "accession": "GCA_002236105.1", "taxid": 198618, "species_taxid": 198618, "relation_to_type": "type", "validated": true, "ani": 90.8279, "matched_fragments": 1774, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas reinekei", "strain": "strain=CCUG 53116", "accession": "GCA_008801455.1", "taxid": 395598, "species_taxid": 395598, "relation_to_type": "type", "validated": true, "ani": 87.8321, "matched_fragments": 1504, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas reinekei", "strain": "strain=MT1", "accession": "GCA_001945365.1", "taxid": 395598, "species_taxid": 395598, "relation_to_type": "type", "validated": true, "ani": 87.8089, "matched_fragments": 1501, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azerbaijanoccidens", "strain": "strain=SWRI74", "accession": "GCA_019145495.1", "taxid": 2842347, "species_taxid": 2842347, "relation_to_type": "type", "validated": true, "ani": 87.7874, "matched_fragments": 1598, "total_fragments": 2503, "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": 87.7641, "matched_fragments": 1565, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jessenii", "strain": "strain=DSM 17150", "accession": "GCA_002236115.1", "taxid": 77298, "species_taxid": 77298, "relation_to_type": "suspected-type", "validated": true, "ani": 87.7194, "matched_fragments": 1550, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurylsulfatiphila", "strain": "strain=AP3_16", "accession": "GCA_002934665.1", "taxid": 2011015, "species_taxid": 2011015, "relation_to_type": "type", "validated": true, "ani": 87.5496, "matched_fragments": 1570, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azerbaijanoriens", "strain": "strain=SWRI123", "accession": "GCA_019139795.1", "taxid": 2842350, "species_taxid": 2842350, "relation_to_type": "type", "validated": true, "ani": 87.5172, "matched_fragments": 1536, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas laurylsulfativorans", "strain": "strain=AP3_22", "accession": "GCA_002906155.1", "taxid": 1943631, "species_taxid": 1943631, "relation_to_type": "type", "validated": true, "ani": 87.4496, "matched_fragments": 1544, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mohnii", "strain": "strain=DSM 18327", "accession": "GCA_900105115.1", "taxid": 395600, "species_taxid": 395600, "relation_to_type": "type", "validated": true, "ani": 87.368, "matched_fragments": 1570, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lini", "strain": "strain=CCUG 51522", "accession": "GCA_008801525.1", "taxid": 163011, "species_taxid": 163011, "relation_to_type": "type", "validated": true, "ani": 86.5195, "matched_fragments": 1397, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mandelii", "strain": "strain=NBRC 103147", "accession": "GCA_002091695.1", "taxid": 75612, "species_taxid": 75612, "relation_to_type": "suspected-type", "validated": true, "ani": 86.5071, "matched_fragments": 1505, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lini", "strain": "strain=DSM 16768", "accession": "GCA_001042905.1", "taxid": 163011, "species_taxid": 163011, "relation_to_type": "type", "validated": true, "ani": 86.498, "matched_fragments": 1404, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas vancouverensis", "strain": "strain=CCUG 49675", "accession": "GCA_008801375.1", "taxid": 95300, "species_taxid": 95300, "relation_to_type": "type", "validated": true, "ani": 86.4274, "matched_fragments": 1485, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas farris", "strain": "strain=SWRI79", "accession": "GCA_019145235.1", "taxid": 2841207, "species_taxid": 2841207, "relation_to_type": "type", "validated": true, "ani": 86.4162, "matched_fragments": 1397, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pharyngis", "strain": "strain=BML-PP036", "accession": "GCA_021602345.1", "taxid": 2892333, "species_taxid": 2892333, "relation_to_type": "type", "validated": true, "ani": 85.918, "matched_fragments": 1378, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas sputi", "strain": "strain=BML-PP014", "accession": "GCA_021603585.1", "taxid": 2892325, "species_taxid": 2892325, "relation_to_type": "type", "validated": true, "ani": 85.8728, "matched_fragments": 1361, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas ekonensis", "strain": "strain=COR58", "accession": "GCA_019145435.1", "taxid": 2842353, "species_taxid": 2842353, "relation_to_type": "type", "validated": true, "ani": 85.5883, "matched_fragments": 1348, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas neuropathica", "strain": "strain=P155", "accession": "GCA_015461835.1", "taxid": 2730425, "species_taxid": 2730425, "relation_to_type": "type", "validated": true, "ani": 85.1365, "matched_fragments": 1363, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas germanica", "strain": "strain=FIT28", "accession": "GCA_019614655.1", "taxid": 2815720, "species_taxid": 2815720, "relation_to_type": "type", "validated": true, "ani": 84.9999, "matched_fragments": 1383, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas rhizophila", "strain": "strain=S211", "accession": "GCA_003033885.1", "taxid": 2045200, "species_taxid": 2045200, "relation_to_type": "type", "validated": true, "ani": 84.025, "matched_fragments": 1186, "total_fragments": 2503, "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": 83.3702, "matched_fragments": 1195, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas karstica", "strain": "strain=CCM 7891", "accession": "GCA_009707515.1", "taxid": 1055468, "species_taxid": 1055468, "relation_to_type": "type", "validated": true, "ani": 82.9088, "matched_fragments": 1096, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas brassicae", "strain": "strain=MAFF 212427", "accession": "GCA_010671725.1", "taxid": 2708063, "species_taxid": 2708063, "relation_to_type": "type", "validated": true, "ani": 82.048, "matched_fragments": 847, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter gudaonensis", "strain": "strain=CGMCC 1.6294", "accession": "GCA_900115175.1", "taxid": 375760, "species_taxid": 375760, "relation_to_type": "type", "validated": true, "ani": 76.1281, "matched_fragments": 136, "total_fragments": 2503, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001976065.1", "gtdb_species": "s__Pseudomonas_E putida_G", "ani": 99.211, "matched_fragments": 2054, "total_fragments": 2503, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.27", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000282475.1", "gtdb_species": "s__Pseudomonas_E sp000282475", "ani": 91.2428, "matched_fragments": 1687, "total_fragments": 2503, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.45", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002236105.1", "gtdb_species": "s__Pseudomonas_E umsongensis", "ani": 90.8285, "matched_fragments": 1774, "total_fragments": 2503, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.47", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000802965.1", "gtdb_species": "s__Pseudomonas_E fluorescens_A", "ani": 88.3097, "matched_fragments": 1580, "total_fragments": 2503, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_900187565.1", "gtdb_species": "s__Pseudomonas_E sp900187565", "ani": 87.9681, "matched_fragments": 1575, "total_fragments": 2503, "gtdb_taxonomy": 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