| Variant ID: vg1124272163 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24272163 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCCGCGCGCTCGCTCGCTGCCGCCGCCACCCCACTTCCGCTGGTCGTCGCGAGCTCGCCCGCCACTTGCTGCCGCTGCAGCCGCGCTCGCCCACTAACG[T/C]
CGAAAGAGAGGAAGAGAAAAAGGAAAAACGACTGGGATGCAACTGACATGTAGGCTCCATGTAATTTTTTAAACTTTTTTGCTGACTAGGATGCCACGTC
GACGTGGCATCCTAGTCAGCAAAAAAGTTTAAAAAATTACATGGAGCCTACATGTCAGTTGCATCCCAGTCGTTTTTCCTTTTTCTCTTCCTCTCTTTCG[A/G]
CGTTAGTGGGCGAGCGCGGCTGCAGCGGCAGCAAGTGGCGGGCGAGCTCGCGACGACCAGCGGAAGTGGGGTGGCGGCGGCAGCGAGCGAGCGCGCGGGC
| 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 | 84.30% | 15.50% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.90% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 54.00% | 45.80% | 0.20% | 0.00% | NA |
| Aus | 269 | 97.80% | 1.10% | 1.12% | 0.00% | NA |
| Indica I | 595 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.50% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 1.70% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 28.20% | 71.40% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 74.70% | 25.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124272163 | T -> C | LOC_Os11g40674.1 | upstream_gene_variant ; 1453.0bp to feature; MODIFIER | silent_mutation | Average:54.466; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| vg1124272163 | T -> C | LOC_Os11g40650-LOC_Os11g40674 | intergenic_region ; MODIFIER | silent_mutation | Average:54.466; most accessible tissue: Zhenshan97 panicle, score: 74.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124272163 | NA | 4.03E-06 | mr1246_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 |
| vg1124272163 | 8.77E-06 | NA | mr1662_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 |
| vg1124272163 | 4.07E-06 | 7.12E-07 | mr1662_2 | Jap_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 |
| vg1124272163 | NA | 6.77E-06 | mr1693_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 |