| Variant ID: vg0136202716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36202716 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 111. )
TGAAATTCAGAATTAAAAATAAGTAACGTTGAAAGAAGTTTCCATGTAACAACCCAATACGAGATTAATCAAAATTCGAAATAAAAATAAAATAAAATCC[G/A]
AAATTAGAAAAGGAAAGGGGAGTCCAAGTAGGAATACAATTTAAAAATAGCTGAAATTCAGAATTAAAAATAAGTAATATTGAAAGAAGTTTCCATATAA
TTATATGGAAACTTCTTTCAATATTACTTATTTTTAATTCTGAATTTCAGCTATTTTTAAATTGTATTCCTACTTGGACTCCCCTTTCCTTTTCTAATTT[C/T]
GGATTTTATTTTATTTTTATTTCGAATTTTGATTAATCTCGTATTGGGTTGTTACATGGAAACTTCTTTCAACGTTACTTATTTTTAATTCTGAATTTCA
| 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 | 51.70% | 45.50% | 2.69% | 0.17% | NA |
| All Indica | 2759 | 23.60% | 71.80% | 4.46% | 0.18% | NA |
| All Japonica | 1512 | 98.30% | 1.50% | 0.13% | 0.07% | NA |
| Aus | 269 | 55.80% | 43.90% | 0.37% | 0.00% | NA |
| Indica I | 595 | 2.90% | 91.10% | 5.38% | 0.67% | NA |
| Indica II | 465 | 7.10% | 88.60% | 4.09% | 0.22% | NA |
| Indica III | 913 | 39.40% | 56.60% | 3.94% | 0.00% | NA |
| Indica Intermediate | 786 | 30.70% | 64.80% | 4.58% | 0.00% | NA |
| Temperate Japonica | 767 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.20% | 2.40% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 67.80% | 28.90% | 1.11% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136202716 | G -> A | LOC_Os01g62514-LOC_Os01g62520 | intergenic_region ; MODIFIER | silent_mutation | Average:8.323; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0136202716 | G -> DEL | N | N | silent_mutation | Average:8.323; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0136202716 | NA | 3.15E-11 | mr1902 | 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 |
| vg0136202716 | NA | 3.62E-06 | mr1870_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 |