| Variant ID: vg0421093803 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 21093803 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCAGCTCGTTACGTCGTAGACTATTGCAATATACTCCATCCTTCCCTAAATATTTGACACCGTTGACTTTTTTAAATATGTTTGACCGTTCCTTTTATT[C/T]
AAAAACTTTTGTGATATGTGTAAAACTATATGTATATATAAAAGTATATTTAACAATAAATCAAATAATAGAAAAAAAATTAATAATTACTTAAATTTTT
AAAAATTTAAGTAATTATTAATTTTTTTTCTATTATTTGATTTATTGTTAAATATACTTTTATATATACATATAGTTTTACACATATCACAAAAGTTTTT[G/A]
AATAAAAGGAACGGTCAAACATATTTAAAAAAGTCAACGGTGTCAAATATTTAGGGAAGGATGGAGTATATTGCAATAGTCTACGACGTAACGAGCTGAT
| 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 | 81.30% | 12.80% | 0.91% | 5.01% | NA |
| All Indica | 2759 | 73.10% | 21.00% | 1.16% | 4.71% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 54.30% | 7.40% | 2.60% | 35.69% | NA |
| Indica I | 595 | 91.10% | 5.90% | 0.34% | 2.69% | NA |
| Indica II | 465 | 87.10% | 11.20% | 0.00% | 1.72% | NA |
| Indica III | 913 | 59.90% | 30.90% | 0.77% | 8.43% | NA |
| Indica Intermediate | 786 | 66.70% | 26.70% | 2.93% | 3.69% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 90.00% | 6.70% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0421093803 | C -> DEL | N | N | silent_mutation | Average:31.788; most accessible tissue: Callus, score: 52.687 | N | N | N | N |
| vg0421093803 | C -> T | LOC_Os04g34780-LOC_Os04g34800 | intergenic_region ; MODIFIER | silent_mutation | Average:31.788; most accessible tissue: Callus, score: 52.687 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0421093803 | 3.97E-06 | NA | mr1861_2 | 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 |
| vg0421093803 | 9.28E-06 | NA | mr1861_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 |