| Variant ID: vg0915670603 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15670603 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )
TCGCCGTCGTTACTTGAAGCCACTGTCATTGTCGTTGCCGTCGACCTCGTTCTCGTCAGTGTCATGGGGACGAAGGGGGCTAGGGGCGGCTGGATTCGCC[C/T]
GTTCCTGTCACCATCGCCGGAGCCAGATCAGCTGCCACGATGCCTCCTTTCTACCGGATCCGCCGCCACCGCGCCTCCCCACTACCCGATCCTCCGCCGC
GCGGCGGAGGATCGGGTAGTGGGGAGGCGCGGTGGCGGCGGATCCGGTAGAAAGGAGGCATCGTGGCAGCTGATCTGGCTCCGGCGATGGTGACAGGAAC[G/A]
GGCGAATCCAGCCGCCCCTAGCCCCCTTCGTCCCCATGACACTGACGAGAACGAGGTCGACGGCAACGACAATGACAGTGGCTTCAAGTAACGACGGCGA
| 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 | 91.60% | 7.70% | 0.70% | 0.00% | NA |
| All Indica | 2759 | 85.90% | 12.90% | 1.20% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 57.00% | 38.10% | 4.95% | 0.00% | NA |
| Indica III | 913 | 91.70% | 8.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 86.60% | 12.50% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915670603 | C -> T | LOC_Os09g26050-LOC_Os09g26060 | intergenic_region ; MODIFIER | silent_mutation | Average:63.415; most accessible tissue: Zhenshan97 young leaf, score: 83.623 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0915670603 | NA | 5.24E-06 | mr1319 | 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 |
| vg0915670603 | NA | 9.29E-07 | mr1593 | 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 |
| vg0915670603 | 1.55E-06 | NA | mr1655 | 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 |
| vg0915670603 | 5.74E-06 | 5.74E-06 | mr1655 | 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 |