| Variant ID: vg1003861056 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 3861056 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AATATTCCTAGTTCTAGGGAAGATCTTTTAGAGAAGTTAAACATTCAAAAAGATGGACAAAAATCTGTTTTGCTTGCATGCTTAGCTGCAGGCACATGGG[C/T]
GATTTGGCTGATGCGAAACGATTGGGTTTTCAATGGAAAACTAACCTCTGATCCCTCTCATTTGCCTCCAAAGCTGTTTCTTTTCTTCTACAGTGGAGAC
GTCTCCACTGTAGAAGAAAAGAAACAGCTTTGGAGGCAAATGAGAGGGATCAGAGGTTAGTTTTCCATTGAAAACCCAATCGTTTCGCATCAGCCAAATC[G/A]
CCCATGTGCCTGCAGCTAAGCATGCAAGCAAAACAGATTTTTGTCCATCTTTTTGAATGTTTAACTTCTCTAAAAGATCTTCCCTAGAACTAGGAATATT
| 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 | 68.50% | 2.30% | 2.43% | 26.79% | NA |
| All Indica | 2759 | 66.50% | 0.30% | 2.90% | 30.34% | NA |
| All Japonica | 1512 | 80.20% | 5.60% | 1.72% | 12.57% | NA |
| Aus | 269 | 40.10% | 5.60% | 1.12% | 53.16% | NA |
| Indica I | 595 | 73.10% | 0.00% | 1.85% | 25.04% | NA |
| Indica II | 465 | 67.70% | 0.00% | 3.87% | 28.39% | NA |
| Indica III | 913 | 70.00% | 0.30% | 1.97% | 27.71% | NA |
| Indica Intermediate | 786 | 56.70% | 0.50% | 4.20% | 38.55% | NA |
| Temperate Japonica | 767 | 85.80% | 6.50% | 2.48% | 5.22% | NA |
| Tropical Japonica | 504 | 79.00% | 2.20% | 0.79% | 18.06% | NA |
| Japonica Intermediate | 241 | 64.70% | 9.50% | 1.24% | 24.48% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 2.08% | 72.92% | NA |
| Intermediate | 90 | 63.30% | 3.30% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1003861056 | C -> T | LOC_Os10g07310.1 | missense_variant ; p.Ala681Val; MODERATE | nonsynonymous_codon ; A681V | Average:51.363; most accessible tissue: Zhenshan97 young leaf, score: 73.54 | unknown | unknown | DELETERIOUS | 0.02 |
| vg1003861056 | C -> DEL | LOC_Os10g07310.1 | N | frameshift_variant | Average:51.363; most accessible tissue: Zhenshan97 young leaf, score: 73.54 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1003861056 | NA | 7.84E-06 | mr1495 | Jap_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 |
| vg1003861056 | 1.61E-06 | 1.61E-06 | mr1868 | Jap_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 |