| Variant ID: vg0610852431 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10852431 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGTACGATATCGGTGGATATAGGTTTTACACGATGTTCAAGGTCAAGAAAAGCGCAGCTCAGAACAGCGGAGTTCGGGTGGAGGCGTTTGACGCATCAG[A/G]
TGAGAAGAAGTCTTACTACGGGATCATACAGGACATTTGGGAGCTGGACTATGGCCTTAACATACAGATCCCGGTGCTACGATGCCAATGGGTCAGAGAC
GTCTCTGACCCATTGGCATCGTAGCACCGGGATCTGTATGTTAAGGCCATAGTCCAGCTCCCAAATGTCCTGTATGATCCCGTAGTAAGACTTCTTCTCA[T/C]
CTGATGCGTCAAACGCCTCCACCCGAACTCCGCTGTTCTGAGCTGCGCTTTTCTTGACCTTGAACATCGTGTAAAACCTATATCCACCGATATCGTACCC
| 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 | 67.90% | 9.30% | 11.89% | 10.83% | NA |
| All Indica | 2759 | 61.40% | 4.00% | 16.96% | 17.65% | NA |
| All Japonica | 1512 | 74.40% | 20.40% | 4.17% | 1.06% | NA |
| Aus | 269 | 91.40% | 3.30% | 4.83% | 0.37% | NA |
| Indica I | 595 | 40.00% | 6.90% | 20.00% | 33.11% | NA |
| Indica II | 465 | 41.10% | 2.60% | 24.30% | 32.04% | NA |
| Indica III | 913 | 84.60% | 1.60% | 9.20% | 4.60% | NA |
| Indica Intermediate | 786 | 62.70% | 5.30% | 19.34% | 12.60% | NA |
| Temperate Japonica | 767 | 63.90% | 33.40% | 2.09% | 0.65% | NA |
| Tropical Japonica | 504 | 89.10% | 1.40% | 7.74% | 1.79% | NA |
| Japonica Intermediate | 241 | 77.20% | 18.70% | 3.32% | 0.83% | NA |
| VI/Aromatic | 96 | 90.60% | 5.20% | 4.17% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 10.00% | 15.56% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610852431 | A -> G | LOC_Os06g19080.1 | missense_variant ; p.Asp828Gly; MODERATE | nonsynonymous_codon ; D828G | Average:17.266; most accessible tissue: Callus, score: 55.285 | unknown | unknown | TOLERATED | 1.00 |
| vg0610852431 | A -> DEL | LOC_Os06g19080.1 | N | frameshift_variant | Average:17.266; most accessible tissue: Callus, score: 55.285 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610852431 | 2.23E-06 | NA | mr1087 | 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 |
| vg0610852431 | NA | 1.75E-07 | mr1087 | 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 |