Search for Variation information by Variation ID:
Detailed information for vg1117156103:
| Variant ID: vg1117156103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17156103 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.04, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
GCCAGGCATCTTCATCATCATGTAGGTGTAGTGTGGGACGGCCATAAATTTGGCTAAAGCCGGTCGTCCAAGTATAGCATGATATGCTGTCTCAAAATCG[G/T]
CAACTTCGAAACAAACATTTTCTGTGCGAAAACTTTCTCGAGTGCCGAAGGTAACTAGAAGAGTGATCTGGCCGAGTGGTGTAGCTGACAATCCTGGGAT
Reverse complement sequence
ATCCCAGGATTGTCAGCTACACCACTCGGCCAGATCACTCTTCTAGTTACCTTCGGCACTCGAGAAAGTTTTCGCACAGAAAATGTTTGTTTCGAAGTTG[C/A]
CGATTTTGAGACAGCATATCATGCTATACTTGGACGACCGGCTTTAGCCAAATTTATGGCCGTCCCACACTACACCTACATGATGATGAAGATGCCTGGC
Allele Frequencies:
| 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 | 29.10% | 20.60% | 16.04% | 34.24% | NA |
| All Indica | 2759 | 44.20% | 7.40% | 22.91% | 25.55% | NA |
| All Japonica | 1512 | 4.20% | 47.70% | 6.81% | 41.27% | NA |
| Aus | 269 | 21.90% | 11.20% | 3.35% | 63.57% | NA |
| Indica I | 595 | 66.40% | 7.70% | 13.78% | 12.10% | NA |
| Indica II | 465 | 27.70% | 15.90% | 16.77% | 39.57% | NA |
| Indica III | 913 | 40.00% | 0.50% | 34.72% | 24.75% | NA |
| Indica Intermediate | 786 | 42.00% | 9.90% | 19.72% | 28.37% | NA |
| Temperate Japonica | 767 | 1.40% | 85.00% | 0.65% | 12.91% | NA |
| Tropical Japonica | 504 | 8.30% | 4.60% | 17.06% | 70.04% | NA |
| Japonica Intermediate | 241 | 4.60% | 19.10% | 4.98% | 71.37% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 3.12% | 91.67% | NA |
| Intermediate | 90 | 33.30% | 21.10% | 12.22% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117156103 | G -> T | LOC_Os11g29570.1 | missense_variant ; p.Ala722Asp; MODERATE | nonsynonymous_codon ; A722D | Average:16.317; most accessible tissue: Minghui63 young leaf, score: 29.964 | possibly damaging  |
1.741 |
DELETERIOUS | 0.01 |
| vg1117156103 | G -> DEL | LOC_Os11g29570.1 | N | frameshift_variant | Average:16.317; most accessible tissue: Minghui63 young leaf, score: 29.964 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1117156103 | NA | 1.74E-08 | mr1832 | 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 |