| Variant ID: vg0334583436 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34583436 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTATTCTAGGAATGGTTTGCACTTTCGTTTCTCTCTCTCTTGTGGGGATCATTTCTCTTACAGTAAATGTAATGTGATGATACTTTGGCTAAATCATCC[C/T]
AAAACTATAAATTTAAAGTGATATATCACAAAAATAGAGATTTAATAATAAAATTATCATAAAGGCCAAGTATCGCAAAACTACAAATTTACTAATAAAA
TTTTATTAGTAAATTTGTAGTTTTGCGATACTTGGCCTTTATGATAATTTTATTATTAAATCTCTATTTTTGTGATATATCACTTTAAATTTATAGTTTT[G/A]
GGATGATTTAGCCAAAGTATCATCACATTACATTTACTGTAAGAGAAATGATCCCCACAAGAGAGAGAGAAACGAAAGTGCAAACCATTCCTAGAATAAC
| 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 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 91.60% | 8.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 80.70% | 19.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334583436 | C -> T | LOC_Os03g60850-LOC_Os03g60870 | intergenic_region ; MODIFIER | silent_mutation | Average:26.449; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334583436 | 4.23E-06 | 5.73E-09 | mr1970 | 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 |
| vg0334583436 | 1.68E-06 | 1.51E-10 | mr1973 | 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 |
| vg0334583436 | NA | 7.03E-06 | mr1671_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 |
| vg0334583436 | NA | 5.25E-08 | mr1970_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 |
| vg0334583436 | NA | 5.36E-10 | mr1973_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 |