| Variant ID: vg1003509410 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 3509410 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 281. )
CGTATTTCTTTGTGATTCGTGCTTCGCTGGGTGTGAGTTGAACTCTTTGTTTTTTTTCTGGGCTGTGCATTTTGTTTTTGGGCTTGGTTTATACATGGCC[C/T]
GTTTCTGGGTTGTTATGTGGGTCCCACTTGCACTGTTCATTTTCGAAATCCGCGCCTACTTTTTTTGCCTGTTCTATGGGTCCCACCTTGACTTTTTCTC
GAGAAAAAGTCAAGGTGGGACCCATAGAACAGGCAAAAAAAGTAGGCGCGGATTTCGAAAATGAACAGTGCAAGTGGGACCCACATAACAACCCAGAAAC[G/A]
GGCCATGTATAAACCAAGCCCAAAAACAAAATGCACAGCCCAGAAAAAAAACAAAGAGTTCAACTCACACCCAGCGAAGCACGAATCACAAAGAAATACG
| 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 | 91.40% | 5.50% | 3.05% | 0.00% | NA |
| All Indica | 2759 | 86.00% | 9.30% | 4.68% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 84.50% | 3.70% | 11.76% | 0.00% | NA |
| Indica II | 465 | 86.00% | 10.50% | 3.44% | 0.00% | NA |
| Indica III | 913 | 83.10% | 15.40% | 1.42% | 0.00% | NA |
| Indica Intermediate | 786 | 90.50% | 5.70% | 3.82% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 13.54% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1003509410 | C -> T | LOC_Os10g06740-LOC_Os10g06760 | intergenic_region ; MODIFIER | silent_mutation | Average:38.576; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1003509410 | 2.99E-07 | 3.51E-11 | mr1709 | 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 |
| vg1003509410 | 1.89E-07 | 1.61E-11 | mr1709_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 |
| vg1003509410 | NA | 3.30E-06 | mr1866_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 |
| vg1003509410 | NA | 1.18E-06 | mr1878_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 |