Search for Variation information by Variation ID:
Detailed information for vg0221203598:
| Variant ID: vg0221203598 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21203598 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )
Flanking Sequence (100 bp) in Reference Genome:
ATGAAGGAGAGAATGTATAAAATCTTCTCAAATGCAATCATAGTCAGCTATTCACACTTGCTGCCAGTGGTGCCGTACAACGCTTTCAACCCCCCTCCAC[C/T]
GGTATTTATTTAAAATCTCAGCCTTTCTCAAAAGCATGCTTTTAACATCTACAAAATTGATTGAAAACTTGAATCATCATGCCCAGGAATTCGCCTTGAT
Reverse complement sequence
ATCAAGGCGAATTCCTGGGCATGATGATTCAAGTTTTCAATCAATTTTGTAGATGTTAAAAGCATGCTTTTGAGAAAGGCTGAGATTTTAAATAAATACC[G/A]
GTGGAGGGGGGTTGAAAGCGTTGTACGGCACCACTGGCAGCAAGTGTGAATAGCTGACTATGATTGCATTTGAGAAGATTTTATACATTCTCTCCTTCAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.00% | 4.00% | 1.06% | 0.00% | NA |
| All Indica | 2759 | 91.70% | 6.60% | 1.74% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.00% | 2.35% | 0.00% | NA |
| Indica II | 465 | 73.30% | 22.60% | 4.09% | 0.00% | NA |
| Indica III | 913 | 96.50% | 3.20% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 92.40% | 6.10% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 2.22% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221203598 | C -> T | LOC_Os02g35280.1 | missense_variant&splice_region_variant ; p.Pro91Leu; MODERATE | nonsynonymous_codon ; P91L | Average:41.085; most accessible tissue: Zhenshan97 flower, score: 53.595 | benign  |
0.281 |
TOLERATED | 0.08 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0221203598 | NA | 9.74E-06 | mr1069 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0221203598 | NA | 7.31E-08 | mr1077 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0221203598 | NA | 1.53E-06 | mr1441 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0221203598 | 7.97E-06 | NA | mr1609 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0221203598 | NA | 1.65E-06 | mr1609 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |