| Variant ID: vg0117092341 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 17092341 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGGTTTGTCCATCTGTCTGCGGATGATAAGCAGTACTAAAGTTCAGCTTAGAACCCATCTCTTCCTGAAGCTTCTTCCAAAACTTTGAAGTAAACTGACT[A/G]
CCTCGATCAGACACTATTTTCTTAGGGACGCCATGCAAACACACAATCATTGCCATATACAATTCCGCCAACCGACTTCCAGAATATGTTGTCTTTACTG
CAGTAAAGACAACATATTCTGGAAGTCGGTTGGCGGAATTGTATATGGCAATGATTGTGTGTTTGCATGGCGTCCCTAAGAAAATAGTGTCTGATCGAGG[T/C]
AGTCAGTTTACTTCAAAGTTTTGGAAGAAGCTTCAGGAAGAGATGGGTTCTAAGCTGAACTTTAGTACTGCTTATCATCCGCAGACAGATGGACAAACCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.40% | 0.30% | 5.42% | 25.92% | NA |
| All Indica | 2759 | 52.10% | 0.50% | 6.81% | 40.59% | NA |
| All Japonica | 1512 | 97.00% | 0.00% | 0.26% | 2.78% | NA |
| Aus | 269 | 60.20% | 0.40% | 21.93% | 17.47% | NA |
| Indica I | 595 | 41.30% | 0.30% | 6.22% | 52.10% | NA |
| Indica II | 465 | 51.40% | 0.00% | 6.67% | 41.94% | NA |
| Indica III | 913 | 58.90% | 0.70% | 7.23% | 33.19% | NA |
| Indica Intermediate | 786 | 52.80% | 0.60% | 6.87% | 39.69% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.60% | 4.17% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.00% | 3.32% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 5.56% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0117092341 | A -> G | LOC_Os01g31250.1 | synonymous_variant ; p.Gly121Gly; LOW | synonymous_codon | Average:13.094; most accessible tissue: Minghui63 root, score: 33.152 | N | N | N | N |
| vg0117092341 | A -> DEL | LOC_Os01g31250.1 | N | frameshift_variant | Average:13.094; most accessible tissue: Minghui63 root, score: 33.152 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0117092341 | 5.19E-06 | NA | mr1866 | 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 |
| vg0117092341 | 5.15E-07 | 5.15E-07 | mr1866 | 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 |