| Variant ID: vg0808276376 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8276376 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.30, others allele: 0.00, population size: 82. )
AATATCTGGTCCCACCTGTCATACACTCGTTACGTCTTGGAGTCCGTGCTGCAGCTGGCTACAGATTTGTAGCCCGCTGCTCTTCTCTCTTCATTTATCT[T/C]
TTTAAAATATACTTAAAGCTGGCTTAGCCTGCTATTGTACTTGTACCTGCTCTAATGTTACTAATTAGCTAGATCCAGAATTGCCTGTAGAAAATTATGA
TCATAATTTTCTACAGGCAATTCTGGATCTAGCTAATTAGTAACATTAGAGCAGGTACAAGTACAATAGCAGGCTAAGCCAGCTTTAAGTATATTTTAAA[A/G]
AGATAAATGAAGAGAGAAGAGCAGCGGGCTACAAATCTGTAGCCAGCTGCAGCACGGACTCCAAGACGTAACGAGTGTATGACAGGTGGGACCAGATATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.40% | 4.30% | 0.93% | 65.30% | NA |
| All Indica | 2759 | 4.30% | 0.50% | 0.94% | 94.27% | NA |
| All Japonica | 1512 | 81.90% | 7.30% | 0.66% | 10.05% | NA |
| Aus | 269 | 0.70% | 2.20% | 0.00% | 97.03% | NA |
| Indica I | 595 | 8.10% | 0.00% | 1.85% | 90.08% | NA |
| Indica II | 465 | 4.70% | 0.20% | 0.65% | 94.41% | NA |
| Indica III | 913 | 1.00% | 1.00% | 0.11% | 97.92% | NA |
| Indica Intermediate | 786 | 5.10% | 0.40% | 1.40% | 93.13% | NA |
| Temperate Japonica | 767 | 93.60% | 3.90% | 0.00% | 2.48% | NA |
| Tropical Japonica | 504 | 76.00% | 3.00% | 0.99% | 20.04% | NA |
| Japonica Intermediate | 241 | 57.30% | 27.40% | 2.07% | 13.28% | NA |
| VI/Aromatic | 96 | 1.00% | 74.00% | 5.21% | 19.79% | NA |
| Intermediate | 90 | 33.30% | 4.40% | 3.33% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808276376 | T -> C | LOC_Os08g13860.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.447; most accessible tissue: Callus, score: 23.358 | N | N | N | N |
| vg0808276376 | T -> DEL | N | N | silent_mutation | Average:11.447; most accessible tissue: Callus, score: 23.358 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808276376 | 2.54E-06 | 1.89E-09 | mr1829 | 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 |
| vg0808276376 | 3.32E-07 | NA | mr1842 | 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 |
| vg0808276376 | 4.23E-08 | 4.13E-12 | mr1829_2 | 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 |
| vg0808276376 | 3.22E-09 | 4.31E-18 | mr1842_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 |