| Variant ID: vg1116495021 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16495021 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTATTTCAATACCATAAATATATTTAGAAGAGTATTCTAATAAAAGTACAAAGCTTACAAAAGAGAAGAGAAAAGCTACTAGAGCCATAGCCAAACTCTT[C/T]
CGAAGGCTTCCGGACTCCTGATTTCTACTCTATTCCTATTCCACTAGCTAGATACTACTAAGCTAAACTTGAGAGAAATGAGAGAGCTATTGCTTGAGGT
ACCTCAAGCAATAGCTCTCTCATTTCTCTCAAGTTTAGCTTAGTAGTATCTAGCTAGTGGAATAGGAATAGAGTAGAAATCAGGAGTCCGGAAGCCTTCG[G/A]
AAGAGTTTGGCTATGGCTCTAGTAGCTTTTCTCTTCTCTTTTGTAAGCTTTGTACTTTTATTAGAATACTCTTCTAAATATATTTATGGTATTGAAATAC
| 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 | 55.00% | 0.60% | 15.21% | 29.26% | NA |
| All Indica | 2759 | 29.70% | 0.80% | 21.86% | 47.63% | NA |
| All Japonica | 1512 | 94.40% | 0.30% | 4.23% | 1.12% | NA |
| Aus | 269 | 78.10% | 0.00% | 13.75% | 8.18% | NA |
| Indica I | 595 | 19.20% | 0.20% | 11.76% | 68.91% | NA |
| Indica II | 465 | 49.00% | 0.40% | 8.39% | 42.15% | NA |
| Indica III | 913 | 21.60% | 1.90% | 37.24% | 39.32% | NA |
| Indica Intermediate | 786 | 35.60% | 0.40% | 19.59% | 44.40% | NA |
| Temperate Japonica | 767 | 96.90% | 0.30% | 1.56% | 1.30% | NA |
| Tropical Japonica | 504 | 89.50% | 0.00% | 9.33% | 1.19% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.80% | 2.07% | 0.41% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 5.21% | 2.08% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 11.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116495021 | C -> T | LOC_Os11g28590-LOC_Os11g28600 | intergenic_region ; MODIFIER | silent_mutation | Average:13.086; most accessible tissue: Callus, score: 33.295 | N | N | N | N |
| vg1116495021 | C -> DEL | N | N | silent_mutation | Average:13.086; most accessible tissue: Callus, score: 33.295 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116495021 | NA | 6.26E-06 | mr1479 | 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 |
| vg1116495021 | 1.50E-06 | 6.30E-07 | mr1919 | 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 |
| vg1116495021 | 5.01E-06 | NA | mr1526_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 |
| vg1116495021 | 2.89E-06 | 5.59E-08 | mr1526_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 |
| vg1116495021 | 3.96E-06 | NA | mr1607_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 |
| vg1116495021 | NA | 2.19E-06 | mr1726_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 |