| Variant ID: vg0310227268 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 10227268 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 113. )
TGAAAAGTAAATGCAAATGCAAAAAGTAAATATTATCTTAATCAACCCCTCCAGTAATCAGTAGTACTCTCTCCGTACTCGTAAAGAAATTCGTTTTGGA[C/T]
AGCGACACGGTCTCTAAAACATAACTTTGACTTCTTGTTTTTATAAAACTATTTATTGAAAAGTTGTATATGTATATTTTTATAAAAGTATTTTTTAAGA
TCTTAAAAAATACTTTTATAAAAATATACATATACAACTTTTCAATAAATAGTTTTATAAAAACAAGAAGTCAAAGTTATGTTTTAGAGACCGTGTCGCT[G/A]
TCCAAAACGAATTTCTTTACGAGTACGGAGAGAGTACTACTGATTACTGGAGGGGTTGATTAAGATAATATTTACTTTTTGCATTTGCATTTACTTTTCA
| 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 | 52.40% | 47.30% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 23.10% | 76.50% | 0.40% | 0.00% | NA |
| All Japonica | 1512 | 98.40% | 1.50% | 0.07% | 0.00% | NA |
| Aus | 269 | 75.80% | 24.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 16.30% | 83.40% | 0.34% | 0.00% | NA |
| Indica II | 465 | 4.90% | 95.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 39.40% | 59.90% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 20.00% | 79.60% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 3.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 3.10% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 37.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0310227268 | C -> T | LOC_Os03g18230.1 | downstream_gene_variant ; 2234.0bp to feature; MODIFIER | silent_mutation | Average:48.043; most accessible tissue: Callus, score: 83.161 | N | N | N | N |
| vg0310227268 | C -> T | LOC_Os03g18250.1 | downstream_gene_variant ; 3344.0bp to feature; MODIFIER | silent_mutation | Average:48.043; most accessible tissue: Callus, score: 83.161 | N | N | N | N |
| vg0310227268 | C -> T | LOC_Os03g18230-LOC_Os03g18250 | intergenic_region ; MODIFIER | silent_mutation | Average:48.043; most accessible tissue: Callus, score: 83.161 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0310227268 | NA | 8.70E-06 | mr1214 | 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 |
| vg0310227268 | NA | 3.09E-06 | mr1306 | 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 |
| vg0310227268 | NA | 1.59E-07 | mr1627 | 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 |
| vg0310227268 | NA | 2.33E-06 | mr1920 | Ind_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 |