| Variant ID: vg1106502273 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6502273 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATTAAATTGATTTAACTTTTATTTAATTTCTAGAAAATGTATTATTAATTGATTTTTATTCCCGAACGAAAATCGGGGCGTTACAATACTGATGGTGGT[C/T]
CAAGCCTGAAGAGGGACTGGTAGGGGTTGCAATTTTCTAGGGCTTTTGCAATGTTCAGGTTTTGCTTGCTGACAAACCTCACAAGAAGCAACATACTTCT
AGAAGTATGTTGCTTCTTGTGAGGTTTGTCAGCAAGCAAAACCTGAACATTGCAAAAGCCCTAGAAAATTGCAACCCCTACCAGTCCCTCTTCAGGCTTG[G/A]
ACCACCATCAGTATTGTAACGCCCCGATTTTCGTTCGGGAATAAAAATCAATTAATAATACATTTTCTAGAAATTAAATAAAAGTTAAATCAATTTAATC
| 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 | 89.00% | 5.00% | 0.85% | 5.10% | NA |
| All Indica | 2759 | 95.70% | 0.60% | 0.51% | 3.19% | NA |
| All Japonica | 1512 | 89.40% | 0.10% | 1.39% | 9.13% | NA |
| Aus | 269 | 19.70% | 79.60% | 0.74% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.90% | 0.00% | 0.00% | 1.08% | NA |
| Indica III | 913 | 92.10% | 0.40% | 0.88% | 6.57% | NA |
| Indica Intermediate | 786 | 94.80% | 1.70% | 0.76% | 2.80% | NA |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.13% | 2.87% | NA |
| Tropical Japonica | 504 | 78.00% | 0.20% | 3.57% | 18.25% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 0.83% | 9.96% | NA |
| VI/Aromatic | 96 | 86.50% | 3.10% | 3.12% | 7.29% | NA |
| Intermediate | 90 | 87.80% | 3.30% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1106502273 | C -> T | LOC_Os11g11694.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.353; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| vg1106502273 | C -> DEL | N | N | silent_mutation | Average:42.353; most accessible tissue: Minghui63 young leaf, score: 60.103 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106502273 | NA | 7.02E-12 | mr1897 | 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 |
| vg1106502273 | 5.95E-08 | NA | mr1248_2 | 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 |
| vg1106502273 | NA | 1.21E-20 | mr1305_2 | 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 |