| Variant ID: vg0326477186 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 26477186 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGCGACGCTGCCGTGCCTCAGCGCCCTAGCCCGTCCCCCTCTCCTCTGCGCTCCGGAGCCGACGGGCAAGGAAGCCCTCCCACCGGGGGCACCTCCTTGC[C/T]
GCTTCTGCGGCCACGATGGCTGCTCTCATCCATTGTCGTCGAGGACAGGAAAAGGGGAGGTGGAGGAAAAGACGGCATCAGAAAAAGGGGCAGTGCCGCC
GGCGGCACTGCCCCTTTTTCTGATGCCGTCTTTTCCTCCACCTCCCCTTTTCCTGTCCTCGACGACAATGGATGAGAGCAGCCATCGTGGCCGCAGAAGC[G/A]
GCAAGGAGGTGCCCCCGGTGGGAGGGCTTCCTTGCCCGTCGGCTCCGGAGCGCAGAGGAGAGGGGGACGGGCTAGGGCGCTGAGGCACGGCAGCGTCGCG
| 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 | 81.80% | 15.70% | 2.50% | 0.00% | NA |
| All Indica | 2759 | 93.90% | 4.30% | 1.81% | 0.00% | NA |
| All Japonica | 1512 | 56.30% | 39.70% | 4.03% | 0.00% | NA |
| Aus | 269 | 97.80% | 1.10% | 1.12% | 0.00% | NA |
| Indica I | 595 | 77.60% | 15.30% | 7.06% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 3.20% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 36.20% | 57.40% | 6.39% | 0.00% | NA |
| Tropical Japonica | 504 | 88.90% | 9.70% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 51.90% | 46.10% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 17.80% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0326477186 | C -> T | LOC_Os03g46820.1 | missense_variant ; p.Pro246Leu; MODERATE | nonsynonymous_codon ; P246L | Average:70.659; most accessible tissue: Zhenshan97 flag leaf, score: 79.935 | unknown | unknown | TOLERATED | 1.00 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0326477186 | NA | 1.24E-12 | mr1056 | 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 |
| vg0326477186 | NA | 1.32E-09 | mr1011_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 |
| vg0326477186 | 4.55E-07 | 5.03E-14 | mr1035_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 |
| vg0326477186 | 2.10E-08 | NA | mr1631_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 |
| vg0326477186 | NA | 5.38E-09 | mr1709_2 | Jap_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 |