| Variant ID: vg1006456883 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 6456883 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGGACACTCTACTCATGGCACCACTAGTTTAAATTTAGGTAGATGCTTCGCAATTTAATTAGGTAACATTAGGCGGTTTTACAAGTATAGACTTTGGGAA[A/C]
TATTCATATCACCTGGATACTCTGGAATTGTTGGATTATTGTGGAATTGGATTCACACCGCCCCCTCTATTCAAAATCCCCAAAAGTGGTTTTAGGCTGG
CCAGCCTAAAACCACTTTTGGGGATTTTGAATAGAGGGGGCGGTGTGAATCCAATTCCACAATAATCCAACAATTCCAGAGTATCCAGGTGATATGAATA[T/G]
TTCCCAAAGTCTATACTTGTAAAACCGCCTAATGTTACCTAATTAAATTGCGAAGCATCTACCTAAATTTAAACTAGTGGTGCCATGAGTAGAGTGTCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.40% | 0.20% | 3.66% | 48.73% | NA |
| All Indica | 2759 | 41.50% | 0.40% | 3.41% | 54.77% | NA |
| All Japonica | 1512 | 61.60% | 0.00% | 2.51% | 35.85% | NA |
| Aus | 269 | 23.00% | 0.00% | 13.01% | 63.94% | NA |
| Indica I | 595 | 25.00% | 0.30% | 2.18% | 72.44% | NA |
| Indica II | 465 | 40.00% | 0.20% | 1.94% | 57.85% | NA |
| Indica III | 913 | 56.40% | 0.40% | 4.93% | 38.23% | NA |
| Indica Intermediate | 786 | 37.40% | 0.40% | 3.44% | 58.78% | NA |
| Temperate Japonica | 767 | 81.60% | 0.00% | 0.52% | 17.86% | NA |
| Tropical Japonica | 504 | 30.60% | 0.00% | 5.75% | 63.69% | NA |
| Japonica Intermediate | 241 | 63.10% | 0.00% | 2.07% | 34.85% | NA |
| VI/Aromatic | 96 | 54.20% | 0.00% | 5.21% | 40.62% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 1.11% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1006456883 | A -> C | LOC_Os10g11680.1 | upstream_gene_variant ; 839.0bp to feature; MODIFIER | silent_mutation | Average:7.516; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1006456883 | A -> C | LOC_Os10g11690.1 | upstream_gene_variant ; 331.0bp to feature; MODIFIER | silent_mutation | Average:7.516; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1006456883 | A -> C | LOC_Os10g11680-LOC_Os10g11690 | intergenic_region ; MODIFIER | silent_mutation | Average:7.516; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg1006456883 | A -> DEL | N | N | silent_mutation | Average:7.516; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1006456883 | NA | 2.73E-06 | mr1053_2 | 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 |
| vg1006456883 | NA | 7.83E-06 | mr1138_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 |
| vg1006456883 | 1.49E-06 | NA | mr1147_2 | 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 |
| vg1006456883 | 8.07E-06 | 7.14E-06 | mr1740_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 |