| Variant ID: vg1127963589 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 27963589 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCGCTGGGGAGTCCATGCCTTGTTTTTAAGGGGGTGATTATGATCCAGGAAAGGTGCGCTGTAATGGATTGTGTTGTGCGAGGGGTATTGTCACAGCTC[C/T]
TTTCCGAGGTACCGCGGTGGTATTGAGGCACATGGTGACATGATGTGGGGCTGTGTCTTGTGGGTACAGTGGTACACCTCTGATTAGAGTAAAACTATTC
GAATAGTTTTACTCTAATCAGAGGTGTACCACTGTACCCACAAGACACAGCCCCACATCATGTCACCATGTGCCTCAATACCACCGCGGTACCTCGGAAA[G/A]
GAGCTGTGACAATACCCCTCGCACAACACAATCCATTACAGCGCACCTTTCCTGGATCATAATCACCCCCTTAAAAACAAGGCATGGACTCCCCAGCGAC
| 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 | 69.30% | 4.60% | 4.15% | 21.94% | NA |
| All Indica | 2759 | 70.90% | 7.80% | 5.58% | 15.73% | NA |
| All Japonica | 1512 | 59.40% | 0.10% | 2.51% | 38.03% | NA |
| Aus | 269 | 94.40% | 0.00% | 1.49% | 4.09% | NA |
| Indica I | 595 | 69.60% | 7.70% | 9.08% | 13.61% | NA |
| Indica II | 465 | 58.70% | 8.00% | 6.24% | 27.10% | NA |
| Indica III | 913 | 76.20% | 8.30% | 3.72% | 11.72% | NA |
| Indica Intermediate | 786 | 72.90% | 7.10% | 4.71% | 15.27% | NA |
| Temperate Japonica | 767 | 42.00% | 0.10% | 3.65% | 54.24% | NA |
| Tropical Japonica | 504 | 80.80% | 0.00% | 0.79% | 18.45% | NA |
| Japonica Intermediate | 241 | 70.10% | 0.00% | 2.49% | 27.39% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 86.70% | 1.10% | 0.00% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127963589 | C -> T | LOC_Os11g46150-LOC_Os11g46180 | intergenic_region ; MODIFIER | silent_mutation | Average:17.173; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| vg1127963589 | C -> DEL | N | N | silent_mutation | Average:17.173; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1127963589 | 1.28E-06 | 1.83E-06 | mr1547 | 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 |
| vg1127963589 | NA | 2.81E-06 | mr1547 | 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 |
| vg1127963589 | NA | 4.88E-06 | mr1547_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 |
| vg1127963589 | NA | 6.78E-07 | mr1547_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 |