| Variant ID: vg0211686764 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 11686764 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCGGGAGGGAGGAGGAGATATTTATCTCGATCCGATTCACGCGTACGCCTCGATCTCTCCGCGCATGCCGATCTTTTTTCCCGGTTGGTACACCAACAG[A/G]
GACTAAAGATCAAAAAGTAGCTCTAACCTTTTTAACCGGGACTAAAGATTACGGTTTTTATTGTAACCGGGACTATTGTGGAATTTGGTCGACCAACAAA
TTTGTTGGTCGACCAAATTCCACAATAGTCCCGGTTACAATAAAAACCGTAATCTTTAGTCCCGGTTAAAAAGGTTAGAGCTACTTTTTGATCTTTAGTC[T/C]
CTGTTGGTGTACCAACCGGGAAAAAAGATCGGCATGCGCGGAGAGATCGAGGCGTACGCGTGAATCGGATCGAGATAAATATCTCCTCCTCCCTCCCGGT
| 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 | 70.20% | 10.30% | 11.07% | 8.44% | NA |
| All Indica | 2759 | 72.70% | 0.20% | 13.56% | 13.56% | NA |
| All Japonica | 1512 | 60.40% | 31.30% | 7.94% | 0.26% | NA |
| Aus | 269 | 87.40% | 0.40% | 5.58% | 6.69% | NA |
| Indica I | 595 | 66.10% | 0.00% | 25.55% | 8.40% | NA |
| Indica II | 465 | 67.50% | 0.40% | 15.05% | 16.99% | NA |
| Indica III | 913 | 79.20% | 0.10% | 4.27% | 16.43% | NA |
| Indica Intermediate | 786 | 73.20% | 0.40% | 14.38% | 12.09% | NA |
| Temperate Japonica | 767 | 30.40% | 58.10% | 11.34% | 0.13% | NA |
| Tropical Japonica | 504 | 94.80% | 0.80% | 3.77% | 0.60% | NA |
| Japonica Intermediate | 241 | 84.20% | 10.00% | 5.81% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 6.70% | 14.44% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0211686764 | A -> G | LOC_Os02g19860-LOC_Os02g19880 | intergenic_region ; MODIFIER | silent_mutation | Average:50.19; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0211686764 | A -> DEL | N | N | silent_mutation | Average:50.19; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0211686764 | NA | 3.54E-06 | mr1211 | Jap_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 |
| vg0211686764 | NA | 1.82E-07 | mr1629 | Jap_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 |
| vg0211686764 | 2.15E-06 | 2.14E-06 | mr1703 | 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 |
| vg0211686764 | NA | 3.66E-07 | mr1763 | 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 |