{ "type": "genome", "identifier": "GCF_900114065.1", "organism": "Stutzerimonas kunmingensis", "title": "Stutzerimonas kunmingensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900114065.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216194", "wgs_master": "FORS00000000.1", "refseq_category": "na", "taxid": "1211807", "species_taxid": "1211807", "organism_name": "Stutzerimonas kunmingensis", "infraspecific_name": "strain=DSM 25974", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2663763606 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900114065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/114/065/GCF_900114065.1_IMG-taxon_2663763606_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4654543", "genome_size_ungapped": "4654263", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900114065.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "4421", "protein_coding_gene_count": "4273", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Stutzerimonas kunmingensis" ], "sample_taxid": [ "1211807" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.297 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)": "4654543", "Number of Sequences": "33", "Longest Sequences (bp)": "889916", "N50 (bp)": "480906", "Gap Ratio (%)": "0.006016", "GCcontent (%)": "62.6", "Number of CDSs": "4356", "Average Protein Length": "316.5", "Coding Ratio (%)": "88.9", "Number of rRNAs": "4", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_900114065.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1534, "total_fragments": 1535, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_024397575.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 99.9761, "matched_fragments": 1507, "total_fragments": 1535, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Stutzerimonas chloritidismutans", "strain": "strain=AW-1", "accession": "GCA_000495915.1", "taxid": 203192, "species_taxid": 203192, "relation_to_type": "type", "validated": true, "ani": 96.7998, "matched_fragments": 1285, "total_fragments": 1535, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Pseudomonas songnenensis", "strain": "strain=DSM 27560T", "accession": "GCA_024448495.1", "taxid": 1176259, "species_taxid": 1176259, "relation_to_type": "type", "validated": true, "ani": 89.156, "matched_fragments": 1219, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas songnenensis", "strain": "strain=NEAU-ST5-5", "accession": "GCA_003696315.1", "taxid": 1176259, "species_taxid": 1176259, "relation_to_type": "type", "validated": true, "ani": 89.121, "matched_fragments": 1220, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=DNSP21", "accession": "GCA_002890935.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 88.7485, "matched_fragments": 1218, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas frequens", "strain": "strain=FDAARGOS_877", "accession": "GCA_016028515.1", "taxid": 2968969, "species_taxid": 2968969, "relation_to_type": "type", "validated": true, "ani": 88.7217, "matched_fragments": 1242, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas stutzeri", "strain": "strain=FDAARGOS_875", "accession": "GCA_016028655.1", "taxid": 316, "species_taxid": 316, "relation_to_type": "type", "validated": true, "ani": 87.7093, "matched_fragments": 1240, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas stutzeri", "strain": "strain=CGMCC 1.1803", "accession": "GCA_000219605.1", "taxid": 316, "species_taxid": 316, "relation_to_type": "type", "validated": true, "ani": 87.6852, "matched_fragments": 1258, "total_fragments": 1535, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900114065.1", "gtdb_species": "s__Pseudomonas_A kunmingensis", "ani": 100.0, "matched_fragments": 1534, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.08, "mean_intra_species_ani": "97.31", "min_intra_species_ani": "97.18", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_013409135.1", "gtdb_species": "s__Pseudomonas_A kunmingensis_A", "ani": 97.0335, "matched_fragments": 1329, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.08, "mean_intra_species_ani": "97.66", "min_intra_species_ani": "97.10", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003935375.1", "gtdb_species": "s__Pseudomonas_A xanthomarina_A", "ani": 96.9753, "matched_fragments": 1325, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0614, "mean_intra_species_ani": "97.25", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_014764705.1", "gtdb_species": "s__Pseudomonas_A sp002692525", "ani": 96.9508, "matched_fragments": 1314, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0332, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_007713455.1", "gtdb_species": "s__Pseudomonas_A sp007713455", "ani": 96.8202, "matched_fragments": 1361, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0636, "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_000495915.1", "gtdb_species": "s__Pseudomonas_A chloritidismutans", "ani": 96.7846, "matched_fragments": 1288, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 96.9847, "mean_intra_species_ani": "97.37", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002929225.1", "gtdb_species": "s__Pseudomonas_A stutzeri_U", "ani": 96.7624, "matched_fragments": 1386, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 97.0711, "mean_intra_species_ani": "97.19", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000935215.1", "gtdb_species": "s__Pseudomonas_A stutzeri_AD", "ani": 96.4829, "matched_fragments": 1232, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 96.8359, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "96.93", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000341615.1", "gtdb_species": "s__Pseudomonas_A stutzeri_G", "ani": 93.3631, "matched_fragments": 1271, "total_fragments": 1535, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_002840055.1", "gtdb_species": "s__Pseudomonas_D sp002840055", "ani": 79.852, "matched_fragments": 214, "total_fragments": 1535, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Stutzerimonas", "kunmingensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }