| Variant ID: vg0414476036 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14476036 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.09, others allele: 0.00, population size: 45. )
AAGAATAGAAAAACACGGCATTCTAATAGTATTATAAGTGCAAAACAGAGTATTGTAAAATATAGGAAAAAAGTGTAAAACAAAGAATTGCAAAATATAA[A/G,C]
AAAAACACAGAAATAACCGTTTGATTGGACTGCAGAAAAACGTAGGAATCAGATGAGAGAGATAGACTAAAAGGGAAACTTCTACGAAGTTGGAGCTCTT
AAGAGCTCCAACTTCGTAGAAGTTTCCCTTTTAGTCTATCTCTCTCATCTGATTCCTACGTTTTTCTGCAGTCCAATCAAACGGTTATTTCTGTGTTTTT[T/C,G]
TTATATTTTGCAATTCTTTGTTTTACACTTTTTTCCTATATTTTACAATACTCTGTTTTGCACTTATAATACTATTAGAATGCCGTGTTTTTCTATTCTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.10% | 2.20% | 1.29% | 74.65% | G: 1.78% |
| All Indica | 2759 | 6.70% | 3.70% | 1.20% | 86.12% | G: 2.25% |
| All Japonica | 1512 | 48.20% | 0.00% | 0.20% | 51.06% | G: 0.53% |
| Aus | 269 | 1.50% | 0.00% | 0.74% | 95.54% | G: 2.23% |
| Indica I | 595 | 18.70% | 0.20% | 0.84% | 79.16% | G: 1.18% |
| Indica II | 465 | 4.50% | 0.00% | 1.29% | 87.96% | G: 6.24% |
| Indica III | 913 | 3.00% | 10.20% | 1.53% | 84.88% | G: 0.44% |
| Indica Intermediate | 786 | 3.30% | 1.10% | 1.02% | 91.73% | G: 2.80% |
| Temperate Japonica | 767 | 84.00% | 0.00% | 0.00% | 16.04% | NA |
| Tropical Japonica | 504 | 4.00% | 0.00% | 0.40% | 94.25% | G: 1.39% |
| Japonica Intermediate | 241 | 27.00% | 0.00% | 0.41% | 72.20% | G: 0.41% |
| VI/Aromatic | 96 | 7.30% | 0.00% | 23.96% | 66.67% | G: 2.08% |
| Intermediate | 90 | 26.70% | 1.10% | 0.00% | 65.56% | G: 6.67% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414476036 | A -> C | LOC_Os04g25080-LOC_Os04g25100 | intergenic_region ; MODIFIER | silent_mutation | Average:10.259; most accessible tissue: Callus, score: 39.085 | N | N | N | N |
| vg0414476036 | A -> DEL | N | N | silent_mutation | Average:10.259; most accessible tissue: Callus, score: 39.085 | N | N | N | N |
| vg0414476036 | A -> G | LOC_Os04g25080-LOC_Os04g25100 | intergenic_region ; MODIFIER | silent_mutation | Average:10.259; most accessible tissue: Callus, score: 39.085 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0414476036 | NA | 6.98E-06 | mr1011 | 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 |
| vg0414476036 | NA | 9.51E-07 | mr1330 | Jap_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 |
| vg0414476036 | 7.08E-06 | NA | mr1549 | 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 |
| vg0414476036 | NA | 9.20E-09 | mr1549 | Jap_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 |
| vg0414476036 | NA | 1.66E-12 | mr1741 | 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 |
| vg0414476036 | NA | 4.13E-08 | mr1864 | Jap_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 |
| vg0414476036 | NA | 1.39E-07 | mr1977 | 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 |
| vg0414476036 | NA | 2.22E-06 | mr1966_2 | Jap_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 |