| Variant ID: vg0118783367 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18783367 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CCAAATCGTCTGTGAAAATGCAAATCTTTGCATGCGGCCAGGGCACCCGCATGCGAAAATGGGCGGTCGCTTATACCGGTCGCATGCGAAAATAAATTCA[A/G]
CAAACAAAAAAAAAATAAAATCCAAAGCCCCAAAAAAAAATAAAAATCCAAAAAATCCCAAACCCTAGCCCGTCGTCCACGCCGCACGCCGTCGCCGGCG
CGCCGGCGACGGCGTGCGGCGTGGACGACGGGCTAGGGTTTGGGATTTTTTGGATTTTTATTTTTTTTTGGGGCTTTGGATTTTATTTTTTTTTTGTTTG[T/C]
TGAATTTATTTTCGCATGCGACCGGTATAAGCGACCGCCCATTTTCGCATGCGGGTGCCCTGGCCGCATGCAAAGATTTGCATTTTCACAGACGATTTGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.20% | 11.70% | 0.53% | 40.61% | NA |
| All Indica | 2759 | 31.90% | 1.30% | 0.58% | 66.15% | NA |
| All Japonica | 1512 | 67.50% | 27.60% | 0.20% | 4.70% | NA |
| Aus | 269 | 75.80% | 21.60% | 1.86% | 0.74% | NA |
| Indica I | 595 | 44.90% | 0.30% | 0.17% | 54.62% | NA |
| Indica II | 465 | 36.30% | 0.90% | 0.43% | 62.37% | NA |
| Indica III | 913 | 18.00% | 1.40% | 0.55% | 80.07% | NA |
| Indica Intermediate | 786 | 35.80% | 2.30% | 1.02% | 60.94% | NA |
| Temperate Japonica | 767 | 84.60% | 15.10% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 53.00% | 33.50% | 0.20% | 13.29% | NA |
| Japonica Intermediate | 241 | 43.20% | 55.20% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 72.90% | 26.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 61.10% | 15.60% | 1.11% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118783367 | A -> G | LOC_Os01g34100.1 | downstream_gene_variant ; 1975.0bp to feature; MODIFIER | silent_mutation | Average:40.726; most accessible tissue: Zhenshan97 flag leaf, score: 74.498 | N | N | N | N |
| vg0118783367 | A -> G | LOC_Os01g34110.1 | downstream_gene_variant ; 801.0bp to feature; MODIFIER | silent_mutation | Average:40.726; most accessible tissue: Zhenshan97 flag leaf, score: 74.498 | N | N | N | N |
| vg0118783367 | A -> G | LOC_Os01g34110-LOC_Os01g34120 | intergenic_region ; MODIFIER | silent_mutation | Average:40.726; most accessible tissue: Zhenshan97 flag leaf, score: 74.498 | N | N | N | N |
| vg0118783367 | A -> DEL | N | N | silent_mutation | Average:40.726; most accessible tissue: Zhenshan97 flag leaf, score: 74.498 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0118783367 | 4.55E-06 | NA | mr1621 | 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 |
| vg0118783367 | NA | 3.47E-07 | mr1622 | 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 |
| vg0118783367 | NA | 4.93E-06 | mr1786 | 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 |