| Variant ID: vg0817298678 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17298678 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TAATAAATATCGGCTGCGTTCTCCGCATCTCATACATCCATGACGACCGATCCATCTAATTATATAAAGGCAAAAAATTTACAGATAAAAAAATAGACCG[C/G]
AGGTATTTCATACAAAAGTTTAAATGCATTTGTCTCCCAAAAAAATACAACAATACATGTAACTAGTATGTACAATTGTTTACATGCAAAATTTGCCCAT
ATGGGCAAATTTTGCATGTAAACAATTGTACATACTAGTTACATGTATTGTTGTATTTTTTTGGGAGACAAATGCATTTAAACTTTTGTATGAAATACCT[G/C]
CGGTCTATTTTTTTATCTGTAAATTTTTTGCCTTTATATAATTAGATGGATCGGTCGTCATGGATGTATGAGATGCGGAGAACGCAGCCGATATTTATTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.20% | 8.80% | 12.44% | 40.48% | NA |
| All Indica | 2759 | 29.10% | 0.80% | 12.18% | 57.96% | NA |
| All Japonica | 1512 | 59.70% | 20.30% | 13.23% | 6.81% | NA |
| Aus | 269 | 23.40% | 0.70% | 10.04% | 65.80% | NA |
| Indica I | 595 | 27.70% | 0.80% | 14.79% | 56.64% | NA |
| Indica II | 465 | 15.70% | 1.30% | 8.39% | 74.62% | NA |
| Indica III | 913 | 37.60% | 0.20% | 11.39% | 50.82% | NA |
| Indica Intermediate | 786 | 28.20% | 1.00% | 13.36% | 57.38% | NA |
| Temperate Japonica | 767 | 71.10% | 11.90% | 14.86% | 2.22% | NA |
| Tropical Japonica | 504 | 49.00% | 30.80% | 5.56% | 14.68% | NA |
| Japonica Intermediate | 241 | 45.60% | 25.30% | 24.07% | 4.98% | NA |
| VI/Aromatic | 96 | 6.20% | 74.00% | 13.54% | 6.25% | NA |
| Intermediate | 90 | 36.70% | 18.90% | 13.33% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817298678 | C -> G | LOC_Os08g28350.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.0; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| vg0817298678 | C -> DEL | N | N | silent_mutation | Average:7.0; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0817298678 | 9.63E-06 | NA | mr1157 | 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 |
| vg0817298678 | 6.07E-06 | NA | mr1525 | 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 |
| vg0817298678 | 6.69E-06 | 6.69E-06 | mr1738 | 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 |
| vg0817298678 | 1.34E-06 | NA | mr1852 | 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 |