| Variant ID: vg0825178332 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25178332 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTATCTTGTGAAGTGCCATTTGGATCAAGAGTTGAAAACATTGATTCTTCTCCAGTCATGTGATTTGTGCATCCACTATCAATCACCCAACTTCTTCCAC[C/T]
GGAGACATATTCCTACAAGAGATCAATTTCTAATTTTAGGTACCCATACTTGCTTGGGTCCTCTCATGTTAGTAACAAGTGCCTTAGGCACCCAAAGTAC
GTACTTTGGGTGCCTAAGGCACTTGTTACTAACATGAGAGGACCCAAGCAAGTATGGGTACCTAAAATTAGAAATTGATCTCTTGTAGGAATATGTCTCC[G/A]
GTGGAAGAAGTTGGGTGATTGATAGTGGATGCACAAATCACATGACTGGAGAAGAATCAATGTTTTCAACTCTTGATCCAAATGGCACTTCACAAGATAA
| 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 | 85.60% | 9.40% | 4.85% | 0.21% | NA |
| All Indica | 2759 | 82.60% | 9.10% | 7.97% | 0.36% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 32.70% | 67.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 75.30% | 5.90% | 17.98% | 0.84% | NA |
| Indica II | 465 | 92.00% | 5.40% | 2.37% | 0.22% | NA |
| Indica III | 913 | 81.80% | 10.20% | 7.67% | 0.33% | NA |
| Indica Intermediate | 786 | 83.30% | 12.50% | 4.07% | 0.13% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 5.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 6.70% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0825178332 | C -> T | LOC_Os08g39760.1 | missense_variant ; p.Gly715Ser; MODERATE | nonsynonymous_codon ; G715S | Average:18.122; most accessible tissue: Minghui63 panicle, score: 34.226 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0825178332 | C -> DEL | LOC_Os08g39760.1 | N | frameshift_variant | Average:18.122; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0825178332 | 3.68E-08 | 8.91E-22 | mr1874 | 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 |
| vg0825178332 | 3.54E-08 | 1.58E-12 | mr1874 | 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 |
| vg0825178332 | NA | 4.46E-19 | mr1874_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 |
| vg0825178332 | NA | 1.38E-08 | mr1874_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 |