| Variant ID: vg1206159410 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6159410 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGGTTAGGAAAGGAGAGGGGTATTCTAAAACGACGCCTCCAAGGAGGGGAACGATGCCAAATGGCGTCGCCGTCGTCAGCTGGCCAAACGGCTCGGCAA[A/G]
GCTTTCGCCCGCGATTCCCTGTCCAAACCCACACCACCAATCCGCACAAGAAGGATCGTCGTCGGTCAACAACATTGTCCCTTCAAAGATTCGGCCAAGG
CCTTGGCCGAATCTTTGAAGGGACAATGTTGTTGACCGACGACGATCCTTCTTGTGCGGATTGGTGGTGTGGGTTTGGACAGGGAATCGCGGGCGAAAGC[T/C]
TTGCCGAGCCGTTTGGCCAGCTGACGACGGCGACGCCATTTGGCATCGTTCCCCTCCTTGGAGGCGTCGTTTTAGAATACCCCTCTCCTTTCCTAACCAT
| 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 | 57.90% | 6.80% | 1.61% | 33.71% | NA |
| All Indica | 2759 | 78.40% | 6.80% | 0.54% | 14.21% | NA |
| All Japonica | 1512 | 26.90% | 0.80% | 3.24% | 69.11% | NA |
| Aus | 269 | 8.60% | 43.90% | 2.97% | 44.61% | NA |
| Indica I | 595 | 66.20% | 7.40% | 0.67% | 25.71% | NA |
| Indica II | 465 | 81.50% | 3.00% | 0.43% | 15.05% | NA |
| Indica III | 913 | 88.40% | 6.90% | 0.33% | 4.38% | NA |
| Indica Intermediate | 786 | 74.30% | 8.50% | 0.76% | 16.41% | NA |
| Temperate Japonica | 767 | 33.60% | 0.80% | 5.87% | 59.71% | NA |
| Tropical Japonica | 504 | 11.30% | 0.40% | 0.60% | 87.70% | NA |
| Japonica Intermediate | 241 | 37.80% | 1.70% | 0.41% | 60.17% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 54.40% | 3.30% | 3.33% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206159410 | A -> DEL | N | N | silent_mutation | Average:7.51; most accessible tissue: Callus, score: 29.779 | N | N | N | N |
| vg1206159410 | A -> G | LOC_Os12g11400.1 | upstream_gene_variant ; 2749.0bp to feature; MODIFIER | silent_mutation | Average:7.51; most accessible tissue: Callus, score: 29.779 | N | N | N | N |
| vg1206159410 | A -> G | LOC_Os12g11410.1 | intron_variant ; MODIFIER | silent_mutation | Average:7.51; most accessible tissue: Callus, score: 29.779 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206159410 | 4.89E-06 | 4.89E-06 | mr1024 | 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 |
| vg1206159410 | NA | 4.17E-06 | mr1933 | 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 |
| vg1206159410 | 1.51E-07 | 5.96E-08 | mr1940 | Jap_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 |