| Variant ID: vg0330337817 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 30337817 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 117. )
ATGGATTTTAGTGAGGACTGTGAGAATAGTCTTAAAAACACTTTAAATCCTATGGCATCTTCTCCTAACTCTAAGAAAAAGAGTAAAAGGGGGAAAAATA[A/G]
GAAAAATAATAAAAATAGTTTCAAATGAAGGGAATCTTTTGGAATTGTGATGGGTTTAAGGACCAAAAAAACATAAGTTTATTTCTGACTTGACCAAGGA
TCCTTGGTCAAGTCAGAAATAAACTTATGTTTTTTTGGTCCTTAAACCCATCACAATTCCAAAAGATTCCCTTCATTTGAAACTATTTTTATTATTTTTC[T/C]
TATTTTTCCCCCTTTTACTCTTTTTCTTAGAGTTAGGAGAAGATGCCATAGGATTTAAAGTGTTTTTAAGACTATTCTCACAGTCCTCACTAAAATCCAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.10% | 35.90% | 3.22% | 1.78% | NA |
| All Indica | 2759 | 89.10% | 2.50% | 5.33% | 3.04% | NA |
| All Japonica | 1512 | 0.90% | 99.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 98.10% | 0.70% | 1.12% | 0.00% | NA |
| Indica I | 595 | 86.40% | 1.00% | 9.41% | 3.19% | NA |
| Indica II | 465 | 81.70% | 4.90% | 7.74% | 5.59% | NA |
| Indica III | 913 | 94.40% | 1.80% | 2.63% | 1.20% | NA |
| Indica Intermediate | 786 | 89.40% | 3.10% | 3.94% | 3.56% | NA |
| Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 98.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 11.50% | 88.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 47.80% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0330337817 | A -> DEL | N | N | silent_mutation | Average:16.802; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0330337817 | A -> G | LOC_Os03g52900.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.802; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0330337817 | 4.74E-06 | NA | mr1519 | 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 |
| vg0330337817 | 3.72E-06 | NA | mr1865 | 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 |