| Variant ID: vg1214950798 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 14950798 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.13, others allele: 0.00, population size: 107. )
GGTGTGAGAGAGAGAGGGAGTCACGGGTGGCTAGAAAAGAAAACCATGATATTTCGTTATCCCATCAGATGCACGATAGCTAGCATTCTCGCGGTTATAC[C/T]
CCCTAATTGATCGCACACATATATCTATCTATCTATCTATCTATCTATCTATATATATATATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT
AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATATATATATAGATAGATAGATAGATAGATAGATAGATATATGTGTGCGATCAATTAGGG[G/A]
GTATAACCGCGAGAATGCTAGCTATCGTGCATCTGATGGGATAACGAAATATCATGGTTTTCTTTTCTAGCCACCCGTGACTCCCTCTCTCTCTCACACC
| 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 | 75.10% | 5.60% | 2.05% | 17.18% | NA |
| All Indica | 2759 | 68.30% | 2.90% | 0.69% | 28.13% | NA |
| All Japonica | 1512 | 85.80% | 8.60% | 4.43% | 1.19% | NA |
| Aus | 269 | 82.20% | 16.70% | 0.74% | 0.37% | NA |
| Indica I | 595 | 80.30% | 0.30% | 0.17% | 19.16% | NA |
| Indica II | 465 | 59.40% | 9.70% | 0.65% | 30.32% | NA |
| Indica III | 913 | 60.60% | 2.40% | 0.66% | 36.36% | NA |
| Indica Intermediate | 786 | 73.50% | 1.30% | 1.15% | 24.05% | NA |
| Temperate Japonica | 767 | 96.50% | 1.40% | 1.56% | 0.52% | NA |
| Tropical Japonica | 504 | 70.60% | 18.50% | 8.53% | 2.38% | NA |
| Japonica Intermediate | 241 | 83.40% | 10.80% | 4.98% | 0.83% | NA |
| VI/Aromatic | 96 | 70.80% | 8.30% | 6.25% | 14.58% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 3.33% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1214950798 | C -> DEL | N | N | silent_mutation | Average:59.94; most accessible tissue: Minghui63 root, score: 86.877 | N | N | N | N |
| vg1214950798 | C -> T | LOC_Os12g25770-LOC_Os12g25790 | intergenic_region ; MODIFIER | silent_mutation | Average:59.94; most accessible tissue: Minghui63 root, score: 86.877 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1214950798 | NA | 8.75E-06 | mr1289 | 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 |
| vg1214950798 | NA | 8.39E-06 | mr1727 | 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 |
| vg1214950798 | 8.49E-08 | 3.35E-07 | mr1898 | 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 |