| Variant ID: vg1108112165 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8112165 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGTCGTTGAAGAAGCTGCAGGAAGACGGCGCCCTTCTCGGTCACGGGACCATAGAGAGAAGCAGGAGGTATTGAACCCAGCATGTCCTGGGCCGCATGGT[C/T]
GCGGTCGAGGACTATATTCTCTGTGGTTTTCTTCCTCCGCCTTCTGAGTTTCTTCTTTTGGTCTTGAATTTCTACGGTCTTTCTTTGCTCCATTTGAACC
GGTTCAAATGGAGCAAAGAAAGACCGTAGAAATTCAAGACCAAAAGAAGAAACTCAGAAGGCGGAGGAAGAAAACCACAGAGAATATAGTCCTCGACCGC[G/A]
ACCATGCGGCCCAGGACATGCTGGGTTCAATACCTCCTGCTTCTCTCTATGGTCCCGTGACCGAGAAGGGCGCCGTCTTCCTGCAGCTTCTTCAACGACG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.60% | 38.20% | 1.08% | 2.20% | NA |
| All Indica | 2759 | 93.80% | 4.50% | 1.34% | 0.40% | NA |
| All Japonica | 1512 | 3.60% | 89.90% | 0.60% | 5.89% | NA |
| Aus | 269 | 26.80% | 71.40% | 1.49% | 0.37% | NA |
| Indica I | 595 | 89.70% | 6.60% | 3.36% | 0.34% | NA |
| Indica II | 465 | 98.10% | 1.50% | 0.00% | 0.43% | NA |
| Indica III | 913 | 97.70% | 1.50% | 0.55% | 0.22% | NA |
| Indica Intermediate | 786 | 89.70% | 8.10% | 1.53% | 0.64% | NA |
| Temperate Japonica | 767 | 1.70% | 98.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 6.00% | 80.40% | 0.99% | 12.70% | NA |
| Japonica Intermediate | 241 | 5.00% | 83.80% | 1.24% | 9.96% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 48.90% | 46.70% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108112165 | C -> T | LOC_Os11g14440.1 | downstream_gene_variant ; 4826.0bp to feature; MODIFIER | silent_mutation | Average:35.016; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg1108112165 | C -> T | LOC_Os11g14460.1 | downstream_gene_variant ; 2786.0bp to feature; MODIFIER | silent_mutation | Average:35.016; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg1108112165 | C -> T | LOC_Os11g14450.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.016; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| vg1108112165 | C -> DEL | N | N | silent_mutation | Average:35.016; most accessible tissue: Zhenshan97 panicle, score: 54.901 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108112165 | NA | 1.06E-06 | mr1058 | 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 |
| vg1108112165 | 3.07E-06 | NA | mr1239 | 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 |
| vg1108112165 | NA | 7.15E-07 | mr1785 | 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 |
| vg1108112165 | NA | 3.12E-15 | mr1916 | 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 |