| Variant ID: vg1119464392 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19464392 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 107. )
GGGCGGAGAAAAAAAAAGGAAAACGGACTGGAAAAAAGGAAAAAAGGGTGAAAAATAAAAAAAGACGGACGAAATTTTTTACGGAAATAGATCCAATCCC[C/T]
AGCATCGTCACGACATAGATATGCCTCGCCGTGTATTTCTACTCTAATTGATTGAAAAAAGCAATTCCCTGTTCATCCTTCATTTATTGCTCAGCTTCTA
TAGAAGCTGAGCAATAAATGAAGGATGAACAGGGAATTGCTTTTTTCAATCAATTAGAGTAGAAATACACGGCGAGGCATATCTATGTCGTGACGATGCT[G/A]
GGGATTGGATCTATTTCCGTAAAAAATTTCGTCCGTCTTTTTTTATTTTTCACCCTTTTTTCCTTTTTTCCAGTCCGTTTTCCTTTTTTTTTCTCCGCCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.90% | 42.10% | 0.19% | 8.80% | NA |
| All Indica | 2759 | 80.40% | 10.70% | 0.25% | 8.63% | NA |
| All Japonica | 1512 | 1.60% | 95.30% | 0.00% | 3.11% | NA |
| Aus | 269 | 11.90% | 45.00% | 0.00% | 43.12% | NA |
| Indica I | 595 | 88.60% | 5.00% | 0.50% | 5.88% | NA |
| Indica II | 465 | 74.80% | 2.60% | 0.00% | 22.58% | NA |
| Indica III | 913 | 79.20% | 17.60% | 0.22% | 2.96% | NA |
| Indica Intermediate | 786 | 79.00% | 11.70% | 0.25% | 9.03% | NA |
| Temperate Japonica | 767 | 1.30% | 96.30% | 0.00% | 2.35% | NA |
| Tropical Japonica | 504 | 2.60% | 96.20% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 0.40% | 90.00% | 0.00% | 9.54% | NA |
| VI/Aromatic | 96 | 2.10% | 96.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 42.20% | 1.11% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119464392 | C -> T | LOC_Os11g32940-LOC_Os11g32950 | intergenic_region ; MODIFIER | silent_mutation | Average:35.161; most accessible tissue: Minghui63 flower, score: 55.591 | N | N | N | N |
| vg1119464392 | C -> DEL | N | N | silent_mutation | Average:35.161; most accessible tissue: Minghui63 flower, score: 55.591 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119464392 | 2.36E-06 | 2.36E-06 | mr1159 | 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 |
| vg1119464392 | NA | 3.22E-06 | mr1754_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 |