| Variant ID: vg0114526827 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526827 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 291. )
GAGAATATGGCATCTCTACCAAATCGACAATATAGCATCTCCAAGGCTTCGAGATAGTACTAGATAATAAATCTGCTTTCCAGGTCGTGTTGATAACAGA[T/A]
CTGCTTGGTTAACTTCCTAAGTATCTGTCTATGTTGCTATGAACAGAACACAATCATGTGCCTTGTGTTCTGGCGAAAAAGGTTACTATCATGTGCGGAT
ATCCGCACATGATAGTAACCTTTTTCGCCAGAACACAAGGCACATGATTGTGTTCTGTTCATAGCAACATAGACAGATACTTAGGAAGTTAACCAAGCAG[A/T]
TCTGTTATCAACACGACCTGGAAAGCAGATTTATTATCTAGTACTATCTCGAAGCCTTGGAGATGCTATATTGTCGATTTGGTAGAGATGCCATATTCTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.70% | 1.30% | 2.79% | 4.13% | NA |
| All Indica | 2759 | 86.00% | 2.30% | 4.78% | 6.92% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 70.90% | 6.70% | 15.29% | 7.06% | NA |
| Indica II | 465 | 94.40% | 0.90% | 1.29% | 3.44% | NA |
| Indica III | 913 | 92.00% | 0.00% | 0.77% | 7.23% | NA |
| Indica Intermediate | 786 | 85.50% | 2.40% | 3.56% | 8.52% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526827 | T -> A | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.895; most accessible tissue: Zhenshan97 flower, score: 77.563 | N | N | N | N |
| vg0114526827 | T -> DEL | N | N | silent_mutation | Average:48.895; most accessible tissue: Zhenshan97 flower, score: 77.563 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114526827 | NA | 1.73E-06 | mr1519 | 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 |
| vg0114526827 | 3.48E-06 | 8.35E-10 | mr1519_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 |