| Variant ID: vg1103239153 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 3239153 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, A: 0.44, others allele: 0.00, population size: 108. )
GGTCTATGCATTGGCTTCGAACTCCAGTCCTAGGCCTTGACGAGGCCTTCTAGCTCCACATTTTGTTTTGCTTTTCTCAGTTTGGGTCCTCTCTTCTCTT[A/G]
TTTGGTGTGTTCAACTTGTCTTGAACTACACTCTCTTCTGGAGTGAATCTTTGTAATAATTGGCTGTAGTTCTTTTTGAACAAAGGCCGGGATATTATAT
ATATAATATCCCGGCCTTTGTTCAAAAAGAACTACAGCCAATTATTACAAAGATTCACTCCAGAAGAGAGTGTAGTTCAAGACAAGTTGAACACACCAAA[T/C]
AAGAGAAGAGAGGACCCAAACTGAGAAAAGCAAAACAAAATGTGGAGCTAGAAGGCCTCGTCAAGGCCTAGGACTGGAGTTCGAAGCCAATGCATAGACC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.90% | 31.10% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 98.00% | 2.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 10.40% | 89.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.10% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.40% | 3.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 23.20% | 76.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 8.30% | 91.30% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 35.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1103239153 | A -> G | LOC_Os11g06650.1 | upstream_gene_variant ; 2607.0bp to feature; MODIFIER | silent_mutation | Average:28.605; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg1103239153 | A -> G | LOC_Os11g06660.1 | downstream_gene_variant ; 4857.0bp to feature; MODIFIER | silent_mutation | Average:28.605; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| vg1103239153 | A -> G | LOC_Os11g06650-LOC_Os11g06660 | intergenic_region ; MODIFIER | silent_mutation | Average:28.605; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1103239153 | NA | 1.61E-12 | mr1170 | 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 |
| vg1103239153 | 4.68E-06 | NA | mr1608 | 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 |
| vg1103239153 | NA | 3.00E-06 | mr1558_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 |
| vg1103239153 | NA | 6.66E-06 | mr1662_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 |