| Variant ID: vg1115833983 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15833983 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGTGAATCTTCTGAACTTCCAGTCCTAGAGGGCAGACTATCTTCTTAGCCTCATATGTTGTCTCGGGCAATTTGTTTCCCTCCGGAAGAATGTTCTTGA[C/T]
GAGTCTCAATTAATCGCCAAATGTCTTGTCACTAACACCATTTTTTGCCTTCCATTGCAAGAACTCCAGAGTGGTATCCAACTTTTTGTGCCCCTGCTCG
CGAGCAGGGGCACAAAAAGTTGGATACCACTCTGGAGTTCTTGCAATGGAAGGCAAAAAATGGTGTTAGTGACAAGACATTTGGCGATTAATTGAGACTC[G/A]
TCAAGAACATTCTTCCGGAGGGAAACAAATTGCCCGAGACAACATATGAGGCTAAGAAGATAGTCTGCCCTCTAGGACTGGAAGTTCAGAAGATTCACGC
| 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 | 86.50% | 0.20% | 5.82% | 7.47% | NA |
| All Indica | 2759 | 78.40% | 0.10% | 9.39% | 12.03% | NA |
| All Japonica | 1512 | 99.00% | 0.30% | 0.33% | 0.40% | NA |
| Aus | 269 | 94.40% | 0.00% | 2.23% | 3.35% | NA |
| Indica I | 595 | 60.20% | 0.30% | 16.97% | 22.52% | NA |
| Indica II | 465 | 85.40% | 0.00% | 10.11% | 4.52% | NA |
| Indica III | 913 | 84.10% | 0.10% | 5.15% | 10.62% | NA |
| Indica Intermediate | 786 | 81.60% | 0.10% | 8.14% | 10.18% | NA |
| Temperate Japonica | 767 | 99.00% | 0.50% | 0.39% | 0.13% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 4.44% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115833983 | C -> T | LOC_Os11g27520.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.858; most accessible tissue: Callus, score: 25.527 | N | N | N | N |
| vg1115833983 | C -> DEL | N | N | silent_mutation | Average:14.858; most accessible tissue: Callus, score: 25.527 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1115833983 | NA | 2.69E-06 | mr1042 | 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 |
| vg1115833983 | 1.16E-06 | 1.54E-06 | mr1707 | Ind_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 |
| vg1115833983 | NA | 2.50E-06 | mr1860_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 |
| vg1115833983 | 7.17E-06 | 1.16E-07 | mr1864_2 | Ind_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 |