| Variant ID: vg0416973093 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 16973093 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACGAACGTGAATGCACTTGTACTAAAAGTGTGAGAACGAACACGTTTATACTAATACGATTTACTGGTAATACATATATGATTATATATGTAACTTGGCC[C/T]
GTTTAGACTAATACATTTTCCTAGTAATGTTGCAGAGAAGACGTTGTCGTCGTCCCTCAAGTCGAAGTGGTAGCTAGCCATCGAAGGAATTCGCGCAGGC
GCCTGCGCGAATTCCTTCGATGGCTAGCTACCACTTCGACTTGAGGGACGACGACAACGTCTTCTCTGCAACATTACTAGGAAAATGTATTAGTCTAAAC[G/A]
GGCCAAGTTACATATATAATCATATATGTATTACCAGTAAATCGTATTAGTATAAACGTGTTCGTTCTCACACTTTTAGTACAAGTGCATTCACGTTCGT
| 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 | 92.60% | 5.40% | 1.99% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 0.70% | 0.94% | 0.00% | NA |
| All Japonica | 1512 | 80.80% | 15.20% | 3.97% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.30% | 0.00% | 2.69% | 0.00% | NA |
| Indica II | 465 | 97.60% | 1.70% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 0.10% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 95.40% | 0.40% | 4.17% | 0.00% | NA |
| Tropical Japonica | 504 | 52.20% | 44.00% | 3.77% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 2.10% | 3.73% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 6.70% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0416973093 | C -> T | LOC_Os04g28650.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.772; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0416973093 | 2.72E-07 | 2.72E-07 | mr1050_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 |
| vg0416973093 | NA | 4.47E-06 | mr1239_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 |
| vg0416973093 | NA | 2.38E-06 | mr1723_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 |