{ "type": "genome", "identifier": "GCF_003244875.1", "organism": "Stenotrophomonas sepilia", "title": "Stenotrophomonas sepilia", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003244875.1", "bioproject": "PRJNA224116", "biosample": "SAMN04978501", "wgs_master": "LXXZ00000000.1", "refseq_category": "na", "taxid": "2860290", "species_taxid": "2860290", "organism_name": "Stenotrophomonas sepilia", "infraspecific_name": "strain=SM16975", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/18", "asm_name": "ASM324487v1", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_003244875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/244/875/GCF_003244875.1_ASM324487v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4582432", "genome_size_ungapped": "4582432", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "119", "contig_count": "119", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003244875.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "4307", "protein_coding_gene_count": "4154", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-18", "dateModified": "2018-06-18", "datePublished": "2018-06-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Stenotrophomonas sepilia" ], "sample_taxid": [ "2860290" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.258 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4582432", "Number of Sequences": "119", "Longest Sequences (bp)": "349174", "N50 (bp)": "83180", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.4", "Number of CDSs": "4239", "Average Protein Length": "319.4", "Coding Ratio (%)": "88.6", "Number of rRNAs": "5", "Number of tRNAs": "72", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Stenotrophomonas sepilia", "strain": "strain=SM16975", "accession": "GCA_003244875.1", "taxid": 2860290, "species_taxid": 2860290, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1466, "total_fragments": 1471, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "[Pseudomonas] hibiscicola", "strain": "strain=ATCC 19867", "accession": "GCA_000382065.1", "taxid": 86189, "species_taxid": 86189, "relation_to_type": "type", "validated": true, "ani": 92.7836, "matched_fragments": 1232, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas pavanii", "strain": "strain=LMG 25348", "accession": "GCA_900101175.1", "taxid": 487698, "species_taxid": 487698, "relation_to_type": "type", "validated": true, "ani": 92.7097, "matched_fragments": 1248, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas pavanii", "strain": "strain=DSM 25135", "accession": "GCA_001431565.1", "taxid": 487698, "species_taxid": 487698, "relation_to_type": "type", "validated": true, "ani": 92.6948, "matched_fragments": 1198, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas maltophilia", "strain": "strain=NCTC10257", "accession": "GCA_900186865.1", "taxid": 40324, "species_taxid": 40324, "relation_to_type": "type", "validated": true, "ani": 91.9602, "matched_fragments": 1297, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas maltophilia", "strain": "strain=ATCC 13637", "accession": "GCA_001997185.1", "taxid": 40324, "species_taxid": 40324, "relation_to_type": "type", "validated": true, "ani": 91.9343, "matched_fragments": 1241, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas maltophilia", "strain": "strain=NBRC 14161", "accession": "GCA_001591205.1", "taxid": 40324, "species_taxid": 40324, "relation_to_type": "type", "validated": true, "ani": 91.9307, "matched_fragments": 1235, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas maltophilia", "strain": "strain=MTCC 434", "accession": "GCA_000597745.1", "taxid": 40324, "species_taxid": 40324, "relation_to_type": "type", "validated": true, "ani": 91.8292, "matched_fragments": 1185, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas pennii", "strain": "strain=Sa5BUN4", "accession": "GCA_014836545.1", "taxid": 2762239, "species_taxid": 2762239, "relation_to_type": "type", "validated": true, "ani": 84.3565, "matched_fragments": 885, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas acidaminiphila", "strain": "strain=DSM 13117", "accession": "GCA_024221815.1", "taxid": 128780, "species_taxid": 128780, "relation_to_type": "type", "validated": true, "ani": 83.6482, "matched_fragments": 779, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stenotrophomonas pictorum", "strain": "strain=JCM 9942", "accession": "GCA_001310775.1", "taxid": 86184, "species_taxid": 86184, "relation_to_type": "type", "validated": true, "ani": 83.1146, "matched_fragments": 483, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas indica", "strain": "strain=PPL560", "accession": "GCA_022669045.1", "taxid": 2912242, "species_taxid": 2912242, "relation_to_type": "type", "validated": true, "ani": 82.5947, "matched_fragments": 825, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas translucens", "strain": "strain=ATCC 19319", "accession": "GCA_020880735.1", "taxid": 343, "species_taxid": 343, "relation_to_type": "type", "validated": true, "ani": 82.3521, "matched_fragments": 663, "total_fragments": 1471, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_014171555.1", "gtdb_species": "s__Stenotrophomonas maltophilia_AK", "ani": 96.1137, "matched_fragments": 1268, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.10", "min_intra_species_ani": "95.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 90, "status": "conclusive" }, { "accession": "GCF_000284595.1", "gtdb_species": "s__Stenotrophomonas maltophilia_F", "ani": 93.2692, "matched_fragments": 1275, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 60, "status": "-" }, { "accession": "GCF_006970445.1", "gtdb_species": "s__Stenotrophomonas maltophilia_AU", "ani": 93.2388, "matched_fragments": 1228, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "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_002192255.1", "gtdb_species": "s__Stenotrophomonas sp002192255", "ani": 92.816, "matched_fragments": 1237, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.64", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000382065.1", "gtdb_species": "s__Stenotrophomonas maltophilia_B", "ani": 92.7885, "matched_fragments": 1231, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.83", "min_intra_species_ani": "97.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_002799245.1", "gtdb_species": "s__Stenotrophomonas maltophilia_S", "ani": 92.7845, "matched_fragments": 1202, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "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_900101175.1", "gtdb_species": "s__Stenotrophomonas pavanii", "ani": 92.7097, "matched_fragments": 1248, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.59", "min_intra_species_ani": "98.08", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_002799155.1", "gtdb_species": "s__Stenotrophomonas maltophilia_R", "ani": 92.4163, "matched_fragments": 1241, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "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": "GCA_001431625.1", "gtdb_species": "s__Stenotrophomonas geniculata", "ani": 92.013, "matched_fragments": 1205, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.51", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.77", "num_clustered_genomes": 45, "status": "-" }, { "accession": "GCF_900186865.1", "gtdb_species": "s__Stenotrophomonas maltophilia", "ani": 91.984, "matched_fragments": 1295, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.99", "min_intra_species_ani": "97.31", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 234, "status": "-" }, { "accession": "GCF_002799165.1", "gtdb_species": "s__Stenotrophomonas maltophilia_Q", "ani": 91.803, "matched_fragments": 1273, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.69", "min_intra_species_ani": "95.30", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.83", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_002138415.1", "gtdb_species": "s__Stenotrophomonas maltophilia_G", "ani": 91.7402, "matched_fragments": 1226, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_004346925.1", "gtdb_species": "s__Stenotrophomonas maltophilia_A", "ani": 91.7354, "matched_fragments": 1217, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.29", "min_intra_species_ani": "95.44", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_006974125.1", "gtdb_species": "s__Stenotrophomonas maltophilia_O", "ani": 91.6661, "matched_fragments": 1191, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_013464915.1", "gtdb_species": "s__Stenotrophomonas maltophilia_AT", "ani": 91.3255, "matched_fragments": 1194, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "98.65", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003028475.1", "gtdb_species": "s__Stenotrophomonas sp003028475", "ani": 90.8041, "matched_fragments": 1167, "total_fragments": 1471, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.27", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.449, "cell_length": 0.058, "doubling_h": null, "growth_tmp": 29.25, "optimum_tmp": 29.25, "optimum_ph": 7.55, "genome_size": 3972347.116, "gc_content": 66.029, "coding_genes": 3882.468, "rRNA16S_genes": 3.25, "tRNA_genes": 69.675, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.625, "range_salinity": 1.0, "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": [ "Stenotrophomonas", "sepilia" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }