| Variant ID: vg0208333146 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8333146 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGAGTATGTTTACAAGTCTTGATGAGGAGAACGGAACTCGTGAGAATATTGTGTTTGGAGATGATGGTAAAGGAAAGGTAATGGGTCTAGGTAAAATTG[C/T]
CATCTCCAATAATCAATCTCTCTCCAATGTTCTTCTTGTCAATTCATTAAGCTACAATTTATTATCCGTTTCTCAATTATGTAAGTTGGGTTACAATTGC
GCAATTGTAACCCAACTTACATAATTGAGAAACGGATAATAAATTGTAGCTTAATGAATTGACAAGAAGAACATTGGAGAGAGATTGATTATTGGAGATG[G/A]
CAATTTTACCTAGACCCATTACCTTTCCTTTACCATCATCTCCAAACACAATATTCTCACGAGTTCCGTTCTCCTCATCAAGACTTGTAAACATACTCCT
| 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 | 94.60% | 4.20% | 0.85% | 0.32% | NA |
| All Indica | 2759 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.80% | 0.50% | 2.65% | 0.99% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 77.20% | 22.80% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 94.10% | 0.70% | 3.52% | 1.69% | NA |
| Tropical Japonica | 504 | 97.20% | 0.20% | 2.18% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208333146 | C -> T | LOC_Os02g14929.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.569; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |
| vg0208333146 | C -> DEL | N | N | silent_mutation | Average:15.569; most accessible tissue: Minghui63 young leaf, score: 26.082 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0208333146 | NA | 5.33E-06 | mr1838 | 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 |
| vg0208333146 | 1.60E-06 | 4.60E-07 | mr1884 | 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 |
| vg0208333146 | 3.30E-06 | 3.30E-06 | mr1884 | 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 |