| Variant ID: vg1123837414 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23837414 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAATTTCTGACTCAGATTCACCATGAGCCATGAAGCAAAAATCAGAGATGTACTCTTCCTTGTCCTTATCTTCATCACTTTTAATATCACCATTGCTTGC[C/A]
GGTTCAAAAGCAGCATAGACTTGATTTAGCACCTTCTTGAGAGCCTCCTTGGATCTTCTTCCCTTGAATGTTGTAACGGGCTTGTTGTCCTTGGTCTTGA
TCAAGACCAAGGACAACAAGCCCGTTACAACATTCAAGGGAAGAAGATCCAAGGAGGCTCTCAAGAAGGTGCTAAATCAAGTCTATGCTGCTTTTGAACC[G/T]
GCAAGCAATGGTGATATTAAAAGTGATGAAGATAAGGACAAGGAAGAGTACATCTCTGATTTTTGCTTCATGGCTCATGGTGAATCTGAGTCAGAAATTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.50% | 0.60% | 2.73% | 40.10% | NA |
| All Indica | 2759 | 37.60% | 0.80% | 3.66% | 57.92% | NA |
| All Japonica | 1512 | 89.70% | 0.30% | 1.39% | 8.66% | NA |
| Aus | 269 | 45.00% | 1.50% | 1.86% | 51.67% | NA |
| Indica I | 595 | 38.70% | 0.30% | 0.84% | 60.17% | NA |
| Indica II | 465 | 21.70% | 0.90% | 4.73% | 72.69% | NA |
| Indica III | 913 | 40.00% | 0.90% | 5.70% | 53.45% | NA |
| Indica Intermediate | 786 | 43.50% | 1.00% | 2.80% | 52.67% | NA |
| Temperate Japonica | 767 | 95.20% | 0.30% | 1.17% | 3.39% | NA |
| Tropical Japonica | 504 | 86.10% | 0.20% | 0.99% | 12.70% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.40% | 2.90% | 17.01% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 1.11% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123837414 | C -> A | LOC_Os11g39960-LOC_Os11g39990 | intergenic_region ; MODIFIER | silent_mutation | Average:25.465; most accessible tissue: Minghui63 flag leaf, score: 52.88 | N | N | N | N |
| vg1123837414 | C -> DEL | N | N | silent_mutation | Average:25.465; most accessible tissue: Minghui63 flag leaf, score: 52.88 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1123837414 | NA | 4.92E-07 | mr1411 | 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 |
| vg1123837414 | NA | 2.69E-06 | mr1560 | 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 |
| vg1123837414 | NA | 3.88E-08 | mr1181_2 | Ind_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 |