| Variant ID: vg1116788419 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16788419 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTTTGGAGGTTTGGTATGTTCAACCGGGGTTGGTTGTTCATATGAGGTTGGGCCTATACAACACGGGTGTGTTGTATGGTGTTTATTTAATATTGACTA[A/G]
TTACTTAACTGTTTTACTATTCTCTTAAATATTAAATGCTGTTTATGCAAATGAGCTATATTATGCCATCCTTTGTTATCCTGTGCACTTGCATATTTGC
GCAAATATGCAAGTGCACAGGATAACAAAGGATGGCATAATATAGCTCATTTGCATAAACAGCATTTAATATTTAAGAGAATAGTAAAACAGTTAAGTAA[T/C]
TAGTCAATATTAAATAAACACCATACAACACACCCGTGTTGTATAGGCCCAACCTCATATGAACAACCAACCCCGGTTGAACATACCAAACCTCCAAACC
| 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 | 36.00% | 32.60% | 21.96% | 9.48% | NA |
| All Indica | 2759 | 4.00% | 53.70% | 30.88% | 11.45% | NA |
| All Japonica | 1512 | 92.70% | 1.40% | 2.51% | 3.44% | NA |
| Aus | 269 | 23.40% | 0.70% | 49.81% | 26.02% | NA |
| Indica I | 595 | 1.80% | 78.50% | 7.56% | 12.10% | NA |
| Indica II | 465 | 1.90% | 49.00% | 35.70% | 13.33% | NA |
| Indica III | 913 | 3.50% | 42.20% | 43.26% | 11.06% | NA |
| Indica Intermediate | 786 | 7.40% | 51.00% | 31.30% | 10.31% | NA |
| Temperate Japonica | 767 | 96.50% | 1.70% | 0.91% | 0.91% | NA |
| Tropical Japonica | 504 | 88.90% | 1.20% | 3.57% | 6.35% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.80% | 5.39% | 5.39% | NA |
| VI/Aromatic | 96 | 94.80% | 2.10% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 36.70% | 12.22% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116788419 | A -> DEL | N | N | silent_mutation | Average:19.068; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| vg1116788419 | A -> G | LOC_Os11g29000.1 | upstream_gene_variant ; 3773.0bp to feature; MODIFIER | silent_mutation | Average:19.068; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| vg1116788419 | A -> G | LOC_Os11g29014.1 | downstream_gene_variant ; 3555.0bp to feature; MODIFIER | silent_mutation | Average:19.068; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| vg1116788419 | A -> G | LOC_Os11g29000-LOC_Os11g29014 | intergenic_region ; MODIFIER | silent_mutation | Average:19.068; most accessible tissue: Zhenshan97 root, score: 36.298 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116788419 | NA | 1.14E-11 | mr1636 | 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 |
| vg1116788419 | NA | 6.95E-16 | mr1842 | 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 |
| vg1116788419 | NA | 7.18E-11 | mr1216_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 |
| vg1116788419 | NA | 3.38E-08 | mr1600_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 |
| vg1116788419 | NA | 3.56E-08 | mr1804_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 |