| Variant ID: vg0808439427 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8439427 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAAATTAAAGAATACTAAAAGATGAGTTTAGAGTCCACATAGAAATACAATTAGAAATAATAAAAATTTAAAAATAAAAATAAATAATATTGGAAGAAGA[G/T,A]
CATAGAGTCTATATAGAAATACAATTTACAGAAAATTCGGAATTAAAAAAAAGAAAATATTAAAAGATAAGTCTAGAGTCCATATAGGAATATATATAAT
ATTATATATATTCCTATATGGACTCTAGACTTATCTTTTAATATTTTCTTTTTTTTAATTCCGAATTTTCTGTAAATTGTATTTCTATATAGACTCTATG[C/A,T]
TCTTCTTCCAATATTATTTATTTTTATTTTTAAATTTTTATTATTTCTAATTGTATTTCTATGTGGACTCTAAACTCATCTTTTAGTATTCTTTAATTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.70% | 22.30% | 1.44% | 2.58% | A: 0.02% |
| All Indica | 2759 | 64.50% | 30.00% | 1.96% | 3.52% | A: 0.04% |
| All Japonica | 1512 | 88.90% | 9.20% | 0.46% | 1.46% | NA |
| Aus | 269 | 96.70% | 0.70% | 1.86% | 0.74% | NA |
| Indica I | 595 | 71.30% | 25.40% | 3.36% | 0.00% | NA |
| Indica II | 465 | 70.30% | 11.00% | 1.94% | 16.77% | NA |
| Indica III | 913 | 52.90% | 45.80% | 1.10% | 0.11% | A: 0.11% |
| Indica Intermediate | 786 | 69.30% | 26.50% | 1.91% | 2.29% | NA |
| Temperate Japonica | 767 | 96.10% | 0.80% | 0.65% | 2.48% | NA |
| Tropical Japonica | 504 | 81.70% | 17.70% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 80.90% | 18.30% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 33.30% | 66.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 21.10% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808439427 | G -> T | LOC_Os08g14109.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.504; most accessible tissue: Callus, score: 25.393 | N | N | N | N |
| vg0808439427 | G -> A | LOC_Os08g14109.1 | intron_variant ; MODIFIER | silent_mutation | Average:12.504; most accessible tissue: Callus, score: 25.393 | N | N | N | N |
| vg0808439427 | G -> DEL | N | N | silent_mutation | Average:12.504; most accessible tissue: Callus, score: 25.393 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808439427 | 8.86E-07 | NA | mr1888_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 |
| vg0808439427 | 1.18E-07 | 8.51E-09 | mr1888_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 |