| Variant ID: vg1118814088 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18814088 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 111. )
TAATTAAGTACTACTATTAACTGTTATAAACTTAAAAAAAAGATTTATTTGACTTTTTAACGAACTTACATAGATTTTTTTAATCAAAGAACTACTCCCT[C/T]
CATTCCAAAATATAAGACACAACCACCCTTAACCTAAAGACTAAGAAACAATTATTATCACCTCTTCGTTTGAATCAATCCAACTAATACAATATATGCA
TGCATATATTGTATTAGTTGGATTGATTCAAACGAAGAGGTGATAATAATTGTTTCTTAGTCTTTAGGTTAAGGGTGGTTGTGTCTTATATTTTGGAATG[G/A]
AGGGAGTAGTTCTTTGATTAAAAAAATCTATGTAAGTTCGTTAAAAAGTCAAATAAATCTTTTTTTTAAGTTTATAACAGTTAATAGTAGTACTTAATTA
| 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 | 71.70% | 23.40% | 0.63% | 4.32% | NA |
| All Indica | 2759 | 56.50% | 35.30% | 1.05% | 7.18% | NA |
| All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 76.60% | 23.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 44.00% | 53.80% | 1.01% | 1.18% | NA |
| Indica II | 465 | 42.80% | 49.20% | 1.72% | 6.24% | NA |
| Indica III | 913 | 66.50% | 21.50% | 0.88% | 11.17% | NA |
| Indica Intermediate | 786 | 62.50% | 29.00% | 0.89% | 7.63% | NA |
| Temperate Japonica | 767 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 55.20% | 39.60% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 75.60% | 22.20% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1118814088 | C -> T | LOC_Os11g31970-LOC_Os11g31980 | intergenic_region ; MODIFIER | silent_mutation | Average:21.891; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
| vg1118814088 | C -> DEL | N | N | silent_mutation | Average:21.891; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118814088 | 6.27E-08 | 4.28E-11 | mr1377 | 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 |
| vg1118814088 | 8.03E-06 | 8.03E-06 | mr1377 | 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 |