| Variant ID: vg1126344683 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26344683 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, G: 0.39, others allele: 0.00, population size: 99. )
TCTTCGTATTTTTGCACATATTTCTTCTCCTATTATCATACTTTATTAGTTAGAAAAGATAATTTTTGTGTTAAACAATTCAACAACTATAACATCTAAA[T/G]
CATACAACTAATTTGTAATTCGCTTTTATCTTTAAAATTATTTATGACTAAATCTACAGCCAAAGACCAAATTTCCACAATAATTAAACTTTGAGAAAAA
TTTTTCTCAAAGTTTAATTATTGTGGAAATTTGGTCTTTGGCTGTAGATTTAGTCATAAATAATTTTAAAGATAAAAGCGAATTACAAATTAGTTGTATG[A/C]
TTTAGATGTTATAGTTGTTGAATTGTTTAACACAAAAATTATCTTTTCTAACTAATAAAGTATGATAATAGGAGAAGAAATATGTGCAAAAATACGAAGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.90% | 17.70% | 1.42% | 3.98% | NA |
| All Indica | 2759 | 81.60% | 14.80% | 0.98% | 2.57% | NA |
| All Japonica | 1512 | 65.20% | 25.50% | 2.58% | 6.75% | NA |
| Aus | 269 | 85.90% | 9.70% | 0.37% | 4.09% | NA |
| Indica I | 595 | 97.50% | 2.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 87.50% | 11.20% | 0.22% | 1.08% | NA |
| Indica III | 913 | 67.80% | 24.40% | 2.19% | 5.59% | NA |
| Indica Intermediate | 786 | 82.20% | 15.50% | 0.38% | 1.91% | NA |
| Temperate Japonica | 767 | 84.70% | 14.90% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 36.10% | 38.10% | 6.55% | 19.25% | NA |
| Japonica Intermediate | 241 | 63.90% | 32.80% | 1.66% | 1.66% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 20.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126344683 | T -> DEL | N | N | silent_mutation | Average:34.119; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg1126344683 | T -> G | LOC_Os11g43650-LOC_Os11g43660 | intergenic_region ; MODIFIER | silent_mutation | Average:34.119; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126344683 | 4.44E-08 | 9.12E-10 | mr1662 | Ind_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 |
| vg1126344683 | NA | 4.03E-08 | mr1158_2 | 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 |