{ "type": "genome", "identifier": "GCF_007858335.1", "organism": "Pseudomonas chlororaphis subsp. chlororaphis", "title": "Pseudomonas chlororaphis subsp. chlororaphis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Technische Universitaet Muenchen", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007858335.1", "bioproject": "PRJNA224116", "biosample": "SAMN12045513", "wgs_master": "VFIN00000000.1", "refseq_category": "na", "taxid": "333", "species_taxid": "587753", "organism_name": "Pseudomonas chlororaphis subsp. chlororaphis", "infraspecific_name": "strain=DSM 50083", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/08/06", "asm_name": "ASM785833v1", "asm_submitter": "Technische Universitaet Muenchen", "gbrs_paired_asm": "GCA_007858335.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/858/335/GCF_007858335.1_ASM785833v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6785600", "genome_size_ungapped": "6785600", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007858335.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "6224", "protein_coding_gene_count": "6076", "non_coding_gene_count": "70", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-08-06", "dateModified": "2019-08-06", "datePublished": "2019-08-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas chlororaphis subsp. chlororaphis" ], "sample_taxid": [ "333" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.879 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)": "6785600", "Number of Sequences": "25", "Longest Sequences (bp)": "1425877", "N50 (bp)": "841352", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.0", "Number of CDSs": "6127", "Average Protein Length": "323.6", "Coding Ratio (%)": "87.7", "Number of rRNAs": "5", "Number of tRNAs": "66", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas chlororaphis subsp. chlororaphis", "strain": "strain=DSM 50083", "accession": "GCA_007858335.1", "taxid": 333, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2249, "total_fragments": 2249, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas chlororaphis subsp. chlororaphis", "strain": "strain=LMG 5004", "accession": "GCA_001269625.1", "taxid": 333, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 99.998, "matched_fragments": 2246, "total_fragments": 2249, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas chlororaphis subsp. chlororaphis", "strain": "strain=DSM 50083", "accession": "GCA_003945765.1", "taxid": 333, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 99.9977, "matched_fragments": 2248, "total_fragments": 2249, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas chlororaphis subsp. chlororaphis", "strain": "", "accession": "GCA_900625015.1", "taxid": 333, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 99.9962, "matched_fragments": 2243, "total_fragments": 2249, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas chlororaphis subsp. chlororaphis", "strain": "strain=ATCC 9446", "accession": "GCA_002095925.1", "taxid": 333, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 99.9919, "matched_fragments": 2237, "total_fragments": 2249, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, "relation_to_type": "type", "validated": true, "ani": 84.0296, "matched_fragments": 1380, "total_fragments": 2249, "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": 82.9557, "matched_fragments": 1113, "total_fragments": 2249, "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": 82.9024, "matched_fragments": 1069, "total_fragments": 2249, "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": 81.9937, "matched_fragments": 1008, "total_fragments": 2249, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas ceruminis", "strain": "strain=BML-PP028", "accession": "GCA_013373895.1", "taxid": 2740516, "species_taxid": 2740516, "relation_to_type": "type", "validated": true, "ani": 81.5282, "matched_fragments": 1007, "total_fragments": 2249, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003945765.1", "gtdb_species": "s__Pseudomonas_E chlororaphis", "ani": 99.9977, "matched_fragments": 2248, "total_fragments": 2249, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.91", "min_intra_species_ani": "95.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 34, "status": "inconclusive" }, { "accession": "GCF_003850345.1", "gtdb_species": "s__Pseudomonas_E chlororaphis_F", "ani": 95.0058, "matched_fragments": 1995, "total_fragments": 2249, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.16", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 82, "status": "inconclusive" }, { "accession": "GCF_900107395.1", "gtdb_species": "s__Pseudomonas_E sp900107395", "ani": 93.4644, "matched_fragments": 1914, "total_fragments": 2249, "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_001921865.1", "gtdb_species": "s__Pseudomonas_E chlororaphis_D", "ani": 91.3674, "matched_fragments": 1819, "total_fragments": 2249, "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_000931465.1", "gtdb_species": "s__Pseudomonas_E sp000931465", "ani": 91.1281, "matched_fragments": 1840, "total_fragments": 2249, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000397205.1", "gtdb_species": "s__Pseudomonas_E protegens", "ani": 86.7181, "matched_fragments": 1628, "total_fragments": 2249, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 76, "status": "-" }, { "accession": "GCF_003363755.1", "gtdb_species": "s__Pseudomonas_E protegens_A", "ani": 86.179, "matched_fragments": 1608, "total_fragments": 2249, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "97.56", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 12, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": 0.0, "doubling_h": -0.025, "growth_tmp": 27.333, "optimum_tmp": 27.667, "optimum_ph": 6.9, "genome_size": 6824747.081, "gc_content": 62.532, "coding_genes": 5951.364, "rRNA16S_genes": 5.0, "tRNA_genes": 68.625, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "chlororaphis", "subsp.", "chlororaphis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }