| Variant ID: vg1128432615 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 28432615 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATTTATAAACTTTGGGTCTCTAAACTTTGGGTCTATAAACTTTAGGTGTATAAACTTTAGGTGCATAAATTTTACTAAAATAGAAAAGTAATGCGGTGC[C/T]
AGAAAAGGAAACGTGGAAGGAGGGAGGGGGGAGGGGATGCGATCGCTACCAGATCGCGGTAGCGATTGATCGCCCATTAGATTTTCCGCCCATAAGTACG
CGTACTTATGGGCGGAAAATCTAATGGGCGATCAATCGCTACCGCGATCTGGTAGCGATCGCATCCCCTCCCCCCTCCCTCCTTCCACGTTTCCTTTTCT[G/A]
GCACCGCATTACTTTTCTATTTTAGTAAAATTTATGCACCTAAAGTTTATACACCTAAAGTTTATAGACCCAAAGTTTAGAGACCCAAAGTTTATAAATC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.70% | 6.00% | 3.96% | 49.39% | NA |
| All Indica | 2759 | 35.20% | 4.60% | 4.02% | 56.18% | NA |
| All Japonica | 1512 | 53.10% | 9.10% | 2.58% | 35.19% | NA |
| Aus | 269 | 25.30% | 0.40% | 11.52% | 62.83% | NA |
| Indica I | 595 | 60.80% | 0.50% | 4.20% | 34.45% | NA |
| Indica II | 465 | 11.80% | 17.80% | 4.73% | 65.59% | NA |
| Indica III | 913 | 33.80% | 0.20% | 2.96% | 62.98% | NA |
| Indica Intermediate | 786 | 31.20% | 5.00% | 4.71% | 59.16% | NA |
| Temperate Japonica | 767 | 63.40% | 0.30% | 1.30% | 35.07% | NA |
| Tropical Japonica | 504 | 36.30% | 22.20% | 3.57% | 37.90% | NA |
| Japonica Intermediate | 241 | 55.60% | 10.00% | 4.56% | 29.88% | NA |
| VI/Aromatic | 96 | 37.50% | 7.30% | 1.04% | 54.17% | NA |
| Intermediate | 90 | 48.90% | 11.10% | 5.56% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1128432615 | C -> T | LOC_Os11g47269.1 | downstream_gene_variant ; 3490.0bp to feature; MODIFIER | silent_mutation | Average:11.794; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1128432615 | C -> T | LOC_Os11g47278.1 | downstream_gene_variant ; 1826.0bp to feature; MODIFIER | silent_mutation | Average:11.794; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1128432615 | C -> T | LOC_Os11g47290.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.794; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1128432615 | C -> DEL | N | N | silent_mutation | Average:11.794; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1128432615 | NA | 5.60E-08 | mr1115_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 |
| vg1128432615 | NA | 7.00E-06 | mr1193_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 |
| vg1128432615 | NA | 8.76E-11 | mr1195_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 |
| vg1128432615 | NA | 5.38E-07 | mr1588_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 |
| vg1128432615 | 4.32E-07 | 4.56E-12 | mr1828_2 | Ind_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 |