{ "type": "genome", "identifier": "GCF_000401255.1", "organism": "Xanthomonas maliensis", "title": "Xanthomonas maliensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Colorado State University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000401255.1", "bioproject": "PRJNA224116", "biosample": "SAMN02469646", "wgs_master": "AQPR00000000.1", "refseq_category": "na", "taxid": "1321368", "species_taxid": "1321368", "organism_name": "Xanthomonas maliensis", "infraspecific_name": "strain=M97", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/05/23", "asm_name": "Xanthomonas sp. 97M", "asm_submitter": "Colorado State University", "gbrs_paired_asm": "GCA_000401255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/401/255/GCF_000401255.1_Xanthomonas_sp._97M", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4965572", "genome_size_ungapped": "4965572", "gc_percent": "66.500000", "replicon_count": "0", "scaffold_count": "1285", "contig_count": "1285", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000401255.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "4862", "protein_coding_gene_count": "4417", "non_coding_gene_count": "52", "pubmed_id": "25588569" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-05-23", "dateModified": "2013-05-23", "datePublished": "2013-05-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthomonas maliensis" ], "sample_taxid": [ "1321368" ], "sample_host_organism": [ "rice" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Mali" ], "sample_host_location_id": [], "data_size": "1.374 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 93.71, "contamination": 3.01, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4965572", "Number of Sequences": "1285", "Longest Sequences (bp)": "35863", "N50 (bp)": "8592", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.7", "Number of CDSs": "3365", "Average Protein Length": "322.3", "Coding Ratio (%)": "65.5", "Number of rRNAs": "1", "Number of tRNAs": "27", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xanthomonas maliensis", "strain": "strain=M97", "accession": "GCA_000401255.1", "taxid": 1321368, "species_taxid": 1321368, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1123, "total_fragments": 1147, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xanthomonas maliensis", "strain": "strain=LMG 27592", "accession": "GCA_009192945.1", "taxid": 1321368, "species_taxid": 1321368, "relation_to_type": "type", "validated": true, "ani": 99.9054, "matched_fragments": 1123, "total_fragments": 1147, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xanthomonas euroxanthea", "strain": "strain=CPBF 424", "accession": "GCA_900476395.1", "taxid": 2259622, "species_taxid": 2259622, "relation_to_type": "type", "validated": true, "ani": 83.893, "matched_fragments": 859, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas euvesicatoria pv. alfalfae", "strain": "strain=CFBP3836", "accession": "GCA_017724035.1", "taxid": 359387, "species_taxid": 456327, "relation_to_type": "pathovar", "validated": true, "ani": 83.4957, "matched_fragments": 882, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas euvesicatoria", "strain": "strain=ATCC 11633", "accession": "GCA_020880415.1", "taxid": 456327, "species_taxid": 456327, "relation_to_type": "type", "validated": true, "ani": 83.4872, "matched_fragments": 871, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas euvesicatoria pv. alfalfae", "strain": "strain=CFBP 3836", "accession": "GCA_000488955.1", "taxid": 359387, "species_taxid": 456327, "relation_to_type": "pathovar", "validated": true, "ani": 83.4766, "matched_fragments": 892, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas phaseoli", "strain": "strain=LMG784", "accession": "GCA_001482665.1", "taxid": 1985254, "species_taxid": 1985254, "relation_to_type": "pathovar", "validated": true, "ani": 83.4326, "matched_fragments": 860, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas floridensis", "strain": "strain=WHRI 8848", "accession": "GCA_001642575.1", "taxid": 1843580, "species_taxid": 1843580, "relation_to_type": "type", "validated": true, "ani": 83.423, "matched_fragments": 878, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas phaseoli", "strain": "strain=LMG 695", "accession": "GCA_001564415.1", "taxid": 1985254, "species_taxid": 1985254, "relation_to_type": "pathovar", "validated": true, "ani": 83.3944, "matched_fragments": 892, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas phaseoli", "strain": "strain=LMG 695", "accession": "GCA_001402235.1", "taxid": 1985254, "species_taxid": 1985254, "relation_to_type": "pathovar", "validated": true, "ani": 83.2958, "matched_fragments": 840, "total_fragments": 1147, "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": 83.2762, "matched_fragments": 852, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas pisi", "strain": "strain=DSM 18956", "accession": "GCA_001010415.1", "taxid": 56457, "species_taxid": 56457, "relation_to_type": "type", "validated": true, "ani": 83.2383, "matched_fragments": 687, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas citri", "strain": "strain=ICMP5732", "accession": "GCA_021474205.1", "taxid": 346, "species_taxid": 346, "relation_to_type": "pathovar", "validated": true, "ani": 83.2092, "matched_fragments": 891, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas citri", "strain": "strain=LMG872", "accession": "GCA_020011215.1", "taxid": 346, "species_taxid": 346, "relation_to_type": "pathovar", "validated": true, "ani": 83.2063, "matched_fragments": 838, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas euvesicatoria", "strain": "strain=LMG 27970", "accession": "GCA_001401555.1", "taxid": 456327, "species_taxid": 456327, "relation_to_type": "type", "validated": true, "ani": 83.1607, "matched_fragments": 688, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas campestris", "strain": "strain=NCPPB 347", "accession": "GCA_020731405.1", "taxid": 339, "species_taxid": 339, "relation_to_type": "pathovar", "validated": true, "ani": 83.0949, "matched_fragments": 844, "total_fragments": 1147, "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": 83.0862, "matched_fragments": 836, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas nasturtii", "strain": "strain=WHRI 8853", "accession": "GCA_001660815.1", "taxid": 1843581, "species_taxid": 1843581, "relation_to_type": "type", "validated": true, "ani": 83.073, "matched_fragments": 828, "total_fragments": 1147, "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": 83.0455, "matched_fragments": 842, "total_fragments": 1147, "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": 81.7557, "matched_fragments": 758, "total_fragments": 1147, "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": 81.3748, "matched_fragments": 617, "total_fragments": 1147, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 93.71, "contamination": 3.01, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009192945.1", "gtdb_species": "s__Xanthomonas maliensis", "ani": 99.9054, "matched_fragments": 1123, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003353015.1", "gtdb_species": "s__Xanthomonas arboricola_E", "ani": 83.9662, "matched_fragments": 856, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_900476395.1", "gtdb_species": "s__Xanthomonas euroxanthea", "ani": 83.8819, "matched_fragments": 860, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_002939785.1", "gtdb_species": "s__Xanthomonas codiaei", "ani": 83.7181, "matched_fragments": 883, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_002940205.1", "gtdb_species": "s__Xanthomonas arboricola_C", "ani": 83.7076, "matched_fragments": 851, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001013475.1", "gtdb_species": "s__Xanthomonas arboricola", "ani": 83.6923, "matched_fragments": 863, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.94", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 117, "status": "-" }, { "accession": "GCF_012848175.1", "gtdb_species": "s__Xanthomonas campestris_C", "ani": 83.6415, "matched_fragments": 870, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_013112235.1", "gtdb_species": "s__Xanthomonas perforans", "ani": 83.5668, "matched_fragments": 890, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "96.72", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.89", "num_clustered_genomes": 246, "status": "-" }, { "accession": "GCF_002940015.1", "gtdb_species": "s__Xanthomonas melonis", "ani": 83.5201, "matched_fragments": 847, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_001642575.1", "gtdb_species": "s__Xanthomonas floridensis", "ani": 83.423, "matched_fragments": 878, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_003999565.1", "gtdb_species": "s__Xanthomonas phaseoli", "ani": 83.3844, "matched_fragments": 887, "total_fragments": 1147, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.19", "min_intra_species_ani": "96.38", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 158, "status": "-" }, { "accession": "GCF_002939885.1", "gtdb_species": "s__Xanthomonas cucurbitae", "ani": 83.2735, "matched_fragments": 799, "total_fragments": 1147, 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