{ "type": "genome", "identifier": "GCF_008119715.3", "organism": "Xanthomonas sontii", "title": "Xanthomonas sontii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008119715.3", "bioproject": "PRJNA224116", "biosample": "SAMN07256652", "wgs_master": "NQYO00000000.2", "refseq_category": "na", "taxid": "2650745", "species_taxid": "2650745", "organism_name": "Xanthomonas sontii", "infraspecific_name": "strain=PPL1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/08/31", "asm_name": "ASM811971v3", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_008119715.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/119/715/GCF_008119715.3_ASM811971v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5043131", "genome_size_ungapped": "5043131", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "191", "contig_count": "191", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008119715.3-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "4387", "protein_coding_gene_count": "4259", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-08-31", "dateModified": "2023-08-31", "datePublished": "2023-08-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthomonas sontii" ], "sample_taxid": [ "2650745" ], "sample_host_organism": [ "Oryza sativa" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.362 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)": "5043131", "Number of Sequences": "191", "Longest Sequences (bp)": "342567", "N50 (bp)": "126396", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.9", "Number of CDSs": "4211", "Average Protein Length": "341.6", "Coding Ratio (%)": "85.6", "Number of rRNAs": "3", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xanthomonas sacchari", "strain": "strain=CFBP4641", "accession": "GCA_002940085.1", "taxid": 56458, "species_taxid": 56458, "relation_to_type": "suspected-type", "validated": true, "ani": 94.745, "matched_fragments": 1427, "total_fragments": 1627, "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": 94.0676, "matched_fragments": 1399, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hyacinthi", "strain": "strain=CFBP1156", "accession": "GCA_002939895.1", "taxid": 56455, "species_taxid": 56455, "relation_to_type": "type", "validated": true, "ani": 88.6416, "matched_fragments": 1143, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hyacinthi", "strain": "strain=CFBP 1156", "accession": "GCA_009769165.1", "taxid": 56455, "species_taxid": 56455, "relation_to_type": "type", "validated": true, "ani": 88.6065, "matched_fragments": 1162, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas translucens", "strain": "strain=DSM 18974", "accession": "GCA_000331775.1", "taxid": 343, "species_taxid": 343, "relation_to_type": "type", "validated": true, "ani": 88.2447, "matched_fragments": 939, "total_fragments": 1627, "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": 88.199, "matched_fragments": 987, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas theicola", "strain": "strain=CFBP 4691", "accession": "GCA_002940605.1", "taxid": 56464, "species_taxid": 56464, "relation_to_type": "type", "validated": true, "ani": 87.9897, "matched_fragments": 997, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas theicola", "strain": "strain=CFBP 4691", "accession": "GCA_014236795.1", "taxid": 56464, "species_taxid": 56464, "relation_to_type": "type", "validated": true, "ani": 87.7614, "matched_fragments": 1075, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas albilineans", "strain": "strain=CFBP2523", "accession": "GCA_002939705.1", "taxid": 29447, "species_taxid": 29447, "relation_to_type": "type", "validated": true, "ani": 84.3924, "matched_fragments": 907, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hydrangeae", "strain": "strain=LMG 31884", "accession": "GCA_905142475.1", "taxid": 2775159, "species_taxid": 2775159, "relation_to_type": "type", "validated": true, "ani": 82.1635, "matched_fragments": 971, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hortorum", "strain": "strain=CFBP 2533", "accession": "GCA_021353095.1", "taxid": 56454, "species_taxid": 56454, "relation_to_type": "pathovar", "validated": true, "ani": 81.994, "matched_fragments": 945, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hortorum", "strain": "strain=CFBP2533", "accession": "GCA_012922215.1", "taxid": 56454, "species_taxid": 56454, "relation_to_type": "pathovar", "validated": true, "ani": 81.9567, "matched_fragments": 941, "total_fragments": 1627, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008119715.1", "gtdb_species": "s__Xanthomonas_A sontii", "ani": 99.8442, "matched_fragments": 1419, "total_fragments": 1627, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.63", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 12, "status": "conclusive" }, { "accession": "GCF_002940085.1", "gtdb_species": "s__Xanthomonas_A sacchari", "ani": 94.7308, "matched_fragments": 1428, "total_fragments": 1627, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001043115.1", "gtdb_species": "s__Xanthomonas_A sp001043115", "ani": 94.1561, "matched_fragments": 1397, "total_fragments": 1627, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.72", "min_intra_species_ani": "96.71", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014199795.1", "gtdb_species": "s__Xanthomonas_A sp014199795", "ani": 93.8576, "matched_fragments": 1404, "total_fragments": 1627, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_014206815.1", "gtdb_species": "s__Xanthomonas_A sacchari_B", "ani": 93.8279, "matched_fragments": 1424, "total_fragments": 1627, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.605, "growth_tmp": 27.096, "optimum_tmp": 27.699, "optimum_ph": null, "genome_size": 4930960.958, "gc_content": 64.384, "coding_genes": 4129.338, "rRNA16S_genes": 1.991, "tRNA_genes": 54.759, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "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": [ "Xanthomonas", "sontii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }