| Variant ID: vg1122195477 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 22195477 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 82. )
GGAGGGAAGCAGCCAGTACTGGAACGAAGAAGAGGGGAACGAGGATCCAAACCAGTATTTCAACGAGGAAGGGAACGTGGAGAGGGATGCGGAGGGGAAC[C/T]
AGGAGGGGCACGTGGAAAGGGATGTGGAGTGGAACCAGGAGGAGGAGGCTAGTGGAAGTCAACCCTCCGTTGGACAGAAGAGGGCATGCGGGCAACGAGG
CCTCGTTGCCCGCATGCCCTCTTCTGTCCAACGGAGGGTTGACTTCCACTAGCCTCCTCCTCCTGGTTCCACTCCACATCCCTTTCCACGTGCCCCTCCT[G/A]
GTTCCCCTCCGCATCCCTCTCCACGTTCCCTTCCTCGTTGAAATACTGGTTTGGATCCTCGTTCCCCTCTTCTTCGTTCCAGTACTGGCTGCTTCCCTCC
| 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 | 31.10% | 28.00% | 18.07% | 22.81% | NA |
| All Indica | 2759 | 16.80% | 25.40% | 27.26% | 30.55% | NA |
| All Japonica | 1512 | 49.30% | 39.60% | 2.12% | 8.99% | NA |
| Aus | 269 | 77.00% | 1.50% | 11.52% | 10.04% | NA |
| Indica I | 595 | 10.80% | 35.00% | 21.51% | 32.77% | NA |
| Indica II | 465 | 10.10% | 2.80% | 41.72% | 45.38% | NA |
| Indica III | 913 | 25.70% | 32.70% | 23.88% | 17.63% | NA |
| Indica Intermediate | 786 | 15.00% | 22.90% | 26.97% | 35.11% | NA |
| Temperate Japonica | 767 | 72.40% | 13.30% | 1.96% | 12.39% | NA |
| Tropical Japonica | 504 | 19.00% | 75.60% | 1.98% | 3.37% | NA |
| Japonica Intermediate | 241 | 39.40% | 47.70% | 2.90% | 9.96% | NA |
| VI/Aromatic | 96 | 20.80% | 4.20% | 23.96% | 51.04% | NA |
| Intermediate | 90 | 35.60% | 21.10% | 17.78% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1122195477 | C -> T | LOC_Os11g37600.1 | stop_gained ; p.Gln49*; HIGH | stop_gained | Average:12.872; most accessible tissue: Callus, score: 24.457 | N | N | N | N |
| vg1122195477 | C -> DEL | LOC_Os11g37600.1 | N | frameshift_variant | Average:12.872; most accessible tissue: Callus, score: 24.457 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1122195477 | 5.96E-06 | NA | mr1798 | 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 |
| vg1122195477 | 2.07E-06 | 2.53E-07 | mr1798 | 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 |