| Variant ID: vg0817104715 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17104715 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 109. )
AACACGAGGAGAAGAAAATTCATGTTCAAGACCTCTTTCGTTGCAAAATTGTTCAAATGAAGCATTCTTTTCAAAGAACCAGGAAATTCAAGATCCAATC[G/A]
AAGAAACAAACCATGAAAGTGTTGAAAAGCTTCGTCCTTAGTTGCTATAAAGAAAACCCAAGAATATCGAGAAAAATCGTCAACAATAACCAACACATAC
GTATGTGTTGGTTATTGTTGACGATTTTTCTCGATATTCTTGGGTTTTCTTTATAGCAACTAAGGACGAAGCTTTTCAACACTTTCATGGTTTGTTTCTT[C/T]
GATTGGATCTTGAATTTCCTGGTTCTTTGAAAAGAATGCTTCATTTGAACAATTTTGCAACGAAAGAGGTCTTGAACATGAATTTTCTTCTCCTCGTGTT
| 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 | 39.10% | 26.30% | 24.29% | 10.30% | NA |
| All Indica | 2759 | 20.50% | 38.90% | 26.89% | 13.77% | NA |
| All Japonica | 1512 | 71.90% | 2.00% | 19.78% | 6.35% | NA |
| Aus | 269 | 37.20% | 36.80% | 26.02% | 0.00% | NA |
| Indica I | 595 | 24.50% | 37.00% | 30.25% | 8.24% | NA |
| Indica II | 465 | 18.30% | 23.20% | 32.69% | 25.81% | NA |
| Indica III | 913 | 17.00% | 50.50% | 21.69% | 10.84% | NA |
| Indica Intermediate | 786 | 22.80% | 36.00% | 26.97% | 14.25% | NA |
| Temperate Japonica | 767 | 79.30% | 0.70% | 13.56% | 6.52% | NA |
| Tropical Japonica | 504 | 62.50% | 3.80% | 26.98% | 6.75% | NA |
| Japonica Intermediate | 241 | 68.00% | 2.50% | 24.48% | 4.98% | NA |
| VI/Aromatic | 96 | 50.00% | 32.30% | 15.62% | 2.08% | NA |
| Intermediate | 90 | 51.10% | 14.40% | 24.44% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817104715 | G -> A | LOC_Os08g28060.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.396; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg0817104715 | G -> DEL | N | N | silent_mutation | Average:16.396; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817104715 | 4.25E-06 | 4.25E-06 | mr1524_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 |
| vg0817104715 | NA | 6.97E-06 | mr1578_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 |