| Variant ID: vg1125073787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25073787 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.01, others allele: 0.00, population size: 186. )
AGTAGCAATCCAAAAAACTGAGAAGCTCGCAGCCGGCGGTTGAGTCAACTACCTGGTCAATGCGAGGCAACCCGAAAGGATCTTTAGGGCAAGATTTGTT[A/G,T]
AGATCAGTGTAATCAACACACATGCGCCATTGCCCTGTTTTCTTCCGAACTAGGACTGGGTTAGCCAGCCAGTCGGGATGAAGGACTTCTTTGATGAAGC
GCTTCATCAAAGAAGTCCTTCATCCCGACTGGCTGGCTAACCCAGTCCTAGTTCGGAAGAAAACAGGGCAATGGCGCATGTGTGTTGATTACACTGATCT[T/C,A]
AACAAATCTTGCCCTAAAGATCCTTTCGGGTTGCCTCGCATTGACCAGGTAGTTGACTCAACCGCCGGCTGCGAGCTTCTCAGTTTTTTGGATTGCTACT
| 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 | 84.30% | 3.10% | 4.49% | 8.06% | T: 0.06% |
| All Indica | 2759 | 75.00% | 4.70% | 7.14% | 13.05% | T: 0.11% |
| All Japonica | 1512 | 99.00% | 0.30% | 0.13% | 0.60% | NA |
| Aus | 269 | 91.80% | 1.10% | 3.35% | 3.72% | NA |
| Indica I | 595 | 48.60% | 12.40% | 14.29% | 24.71% | NA |
| Indica II | 465 | 79.40% | 6.20% | 6.02% | 8.39% | NA |
| Indica III | 913 | 87.30% | 1.00% | 3.72% | 7.89% | T: 0.11% |
| Indica Intermediate | 786 | 78.10% | 2.30% | 6.36% | 12.98% | T: 0.25% |
| Temperate Japonica | 767 | 99.30% | 0.40% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 0.20% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 5.60% | 4.44% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125073787 | A -> T | LOC_Os11g41760.1 | synonymous_variant ; p.Leu1065Leu; LOW | synonymous_codon | Average:14.802; most accessible tissue: Minghui63 flag leaf, score: 26.303 | N | N | N | N |
| vg1125073787 | A -> DEL | LOC_Os11g41760.1 | N | frameshift_variant | Average:14.802; most accessible tissue: Minghui63 flag leaf, score: 26.303 | N | N | N | N |
| vg1125073787 | A -> G | LOC_Os11g41760.1 | synonymous_variant ; p.Leu1065Leu; LOW | synonymous_codon | Average:14.802; most accessible tissue: Minghui63 flag leaf, score: 26.303 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125073787 | 2.00E-06 | NA | mr1943 | 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 |