| Variant ID: vg0335540142 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35540142 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 286. )
AGAGAGAGGGAGCGCGATGCGGATCGGGGAGATGAGAAGGGGTGCGACGGGTGGATCGTGGGAGAAAATCTCATCCGCTGATGCCTGTGAGAGGATCCTC[C/T]
GATGAATGTTAACCATTCGATCGTTCAGGACTCACCACCACCACTACGAATTTTTTAAGTAGTAAAGAAATAGAGCGATAAAAGAATTCACATGATCTTG
CAAGATCATGTGAATTCTTTTATCGCTCTATTTCTTTACTACTTAAAAAATTCGTAGTGGTGGTGGTGAGTCCTGAACGATCGAATGGTTAACATTCATC[G/A]
GAGGATCCTCTCACAGGCATCAGCGGATGAGATTTTCTCCCACGATCCACCCGTCGCACCCCTTCTCATCTCCCCGATCCGCATCGCGCTCCCTCTCTCT
| 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 | 89.00% | 2.80% | 3.22% | 4.99% | NA |
| All Indica | 2759 | 81.40% | 4.60% | 5.47% | 8.52% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 86.90% | 4.30% | 4.30% | 4.52% | NA |
| Indica III | 913 | 63.20% | 7.30% | 10.84% | 18.62% | NA |
| Indica Intermediate | 786 | 85.20% | 5.10% | 4.07% | 5.60% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335540142 | C -> T | LOC_Os03g62820.1 | stop_gained ; p.Arg201*; HIGH | stop_gained | Average:62.189; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| vg0335540142 | C -> DEL | LOC_Os03g62820.1 | N | frameshift_variant | Average:62.189; most accessible tissue: Zhenshan97 panicle, score: 85.254 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0335540142 | 7.89E-06 | 4.55E-06 | mr1119_2 | 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 |
| vg0335540142 | 8.68E-06 | NA | mr1216_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 |
| vg0335540142 | 7.04E-06 | 1.42E-06 | mr1216_2 | 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 |
| vg0335540142 | 3.81E-06 | NA | mr1223_2 | 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 |
| vg0335540142 | 1.71E-06 | 5.60E-06 | mr1223_2 | 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 |