| Variant ID: vg0421169357 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 21169357 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGAGAGATGATGGAAGTGGTGACTTGTCTTTCTATAAGACCTTAGGACTTTTACGTTACACTATACTTGCAATATATACTTACAGGAGTCCTACTCCGGT[A/G]
CTTTCTACTCGGAGTAGAAAGTAATCTAGGCCCTTGATCATATTTAATTGTAGGGTTAAGATCTAGTTCTACTCCTACCAGAATTAGTGGAAGTAGAAAT
ATTTCTACTTCCACTAATTCTGGTAGGAGTAGAACTAGATCTTAACCCTACAATTAAATATGATCAAGGGCCTAGATTACTTTCTACTCCGAGTAGAAAG[T/C]
ACCGGAGTAGGACTCCTGTAAGTATATATTGCAAGTATAGTGTAACGTAAAAGTCCTAAGGTCTTATAGAAAGACAAGTCACCACTTCCATCATCTCTCA
| 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 | 65.00% | 0.60% | 2.22% | 32.16% | NA |
| All Indica | 2759 | 49.60% | 0.80% | 3.26% | 46.28% | NA |
| All Japonica | 1512 | 98.40% | 0.10% | 0.07% | 1.46% | NA |
| Aus | 269 | 33.50% | 1.10% | 3.35% | 62.08% | NA |
| Indica I | 595 | 50.30% | 0.00% | 5.04% | 44.71% | NA |
| Indica II | 465 | 40.40% | 1.10% | 3.87% | 54.62% | NA |
| Indica III | 913 | 52.70% | 0.40% | 1.86% | 45.02% | NA |
| Indica Intermediate | 786 | 51.00% | 1.80% | 3.18% | 44.02% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 0.20% | 0.20% | 4.17% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 55.20% | 0.00% | 1.04% | 43.75% | NA |
| Intermediate | 90 | 81.10% | 1.10% | 4.44% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0421169357 | A -> DEL | N | N | silent_mutation | Average:18.641; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0421169357 | A -> G | LOC_Os04g34860-LOC_Os04g34870 | intergenic_region ; MODIFIER | silent_mutation | Average:18.641; 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 |
|---|---|---|---|---|---|---|
| vg0421169357 | 3.03E-06 | 3.03E-06 | mr1275 | 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 |
| vg0421169357 | NA | 5.15E-06 | mr1960 | 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 |