| Variant ID: vg1106746957 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6746957 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAGCTCCAGTGCCCGAAAGCCTGTTCGATCCGTCAAAATGCATGGTCCAATGCTCTATCTTTTCCTCAGGGGTGTCCTCCTTGCACTCGGTCCACTCGGC[A/G]
ACGAAGTCGGCTAAAGCTTGGGACTTGATCGAAGTTCGTGGCTTGAACGATATGTCCAAAGACATCAGTTCTAAGGCCCATTTGGCGATCCGTCCATTTG
CAAATGGACGGATCGCCAAATGGGCCTTAGAACTGATGTCTTTGGACATATCGTTCAAGCCACGAACTTCGATCAAGTCCCAAGCTTTAGCCGACTTCGT[T/C]
GCCGAGTGGACCGAGTGCAAGGAGGACACCCCTGAGGAAAAGATAGAGCATTGGACCATGCATTTTGACGGATCGAACAGGCTTTCGGGCACTGGAGCTG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.60% | 3.90% | 1.46% | 14.05% | NA |
| All Indica | 2759 | 96.30% | 1.20% | 0.80% | 1.70% | NA |
| All Japonica | 1512 | 48.10% | 9.80% | 2.78% | 39.29% | NA |
| Aus | 269 | 98.50% | 0.00% | 0.37% | 1.12% | NA |
| Indica I | 595 | 91.40% | 3.70% | 2.86% | 2.02% | NA |
| Indica II | 465 | 98.70% | 0.00% | 0.43% | 0.86% | NA |
| Indica III | 913 | 98.70% | 0.20% | 0.11% | 0.99% | NA |
| Indica Intermediate | 786 | 95.80% | 1.10% | 0.25% | 2.80% | NA |
| Temperate Japonica | 767 | 62.70% | 1.30% | 0.26% | 35.72% | NA |
| Tropical Japonica | 504 | 30.20% | 16.10% | 6.35% | 47.42% | NA |
| Japonica Intermediate | 241 | 39.40% | 23.70% | 3.32% | 33.61% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 2.08% | 12.50% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 2.22% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1106746957 | A -> DEL | LOC_Os11g12100.1 | N | frameshift_variant | Average:9.557; most accessible tissue: Callus, score: 39.581 | N | N | N | N |
| vg1106746957 | A -> G | LOC_Os11g12100.1 | synonymous_variant ; p.Val1335Val; LOW | synonymous_codon | Average:9.557; most accessible tissue: Callus, score: 39.581 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106746957 | 1.88E-07 | NA | mr1281 | 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 |
| vg1106746957 | NA | 1.37E-06 | mr1709 | 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 |
| vg1106746957 | 6.79E-06 | NA | mr1737 | 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 |
| vg1106746957 | NA | 2.30E-06 | mr1749 | 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 |