| Variant ID: vg1125935268 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25935268 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTGACGGAACCGATCCCAAGCCCTACATGTGCAGCTGCAAGCTATGATTAATTAATTTTTACCCGAGATCAACATAATAGCAACAGAGTCCCGCGACTTT[G/T]
GAATAAATGGCATTATATTACCTGTCTATCAGTTGGAAGACCTTGTCAAAAACCTTCTCCTCTTTATTCATTGAGTCGTACACAGTGACTCTGCATGCGT
ACGCATGCAGAGTCACTGTGTACGACTCAATGAATAAAGAGGAGAAGGTTTTTGACAAGGTCTTCCAACTGATAGACAGGTAATATAATGCCATTTATTC[C/A]
AAAGTCGCGGGACTCTGTTGCTATTATGTTGATCTCGGGTAAAAATTAATTAATCATAGCTTGCAGCTGCACATGTAGGGCTTGGGATCGGTTCCGTCAA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.50% | 13.60% | 2.26% | 19.59% | NA |
| All Indica | 2759 | 54.50% | 19.10% | 2.39% | 23.99% | NA |
| All Japonica | 1512 | 81.90% | 4.10% | 1.46% | 12.50% | NA |
| Aus | 269 | 56.10% | 15.20% | 4.83% | 23.79% | NA |
| Indica I | 595 | 61.20% | 3.40% | 1.01% | 34.45% | NA |
| Indica II | 465 | 43.90% | 6.70% | 3.23% | 46.24% | NA |
| Indica III | 913 | 51.00% | 35.70% | 3.07% | 10.19% | NA |
| Indica Intermediate | 786 | 59.90% | 19.00% | 2.16% | 18.96% | NA |
| Temperate Japonica | 767 | 76.70% | 0.50% | 1.43% | 21.38% | NA |
| Tropical Japonica | 504 | 87.70% | 10.10% | 0.79% | 1.39% | NA |
| Japonica Intermediate | 241 | 86.70% | 2.90% | 2.90% | 7.47% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 15.60% | 5.56% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125935268 | G -> T | LOC_Os11g43020.1 | intron_variant ; MODIFIER | silent_mutation | Average:28.63; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
| vg1125935268 | G -> DEL | N | N | silent_mutation | Average:28.63; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125935268 | 2.26E-06 | NA | mr1133 | 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 |
| vg1125935268 | NA | 2.56E-07 | mr1133_2 | 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 |
| vg1125935268 | NA | 5.80E-06 | mr1667_2 | 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 |