| Variant ID: vg0221679698 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21679698 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CATGAAATTGTTTCTCTAATTGAGCCCAAGTATGAATAGAATTTGCCGGTAAAGAAGTAAACCATGTAAAAGCATTACTGGATAAAGATAAAGAAAATAA[G/A]
CGCAATTTAAAAGTATCACTATTAGCCTCACCACATTGCGCTAAAAATTGACCTACATGCTCCCATGTGGTCTTACCATCCTCACCACTAAACTTGGTAA
TTACCAAGTTTAGTGGTGAGGATGGTAAGACCACATGGGAGCATGTAGGTCAATTTTTAGCGCAATGTGGTGAGGCTAATAGTGATACTTTTAAATTGCG[C/T]
TTATTTTCTTTATCTTTATCCAGTAATGCTTTTACATGGTTTACTTCTTTACCGGCAAATTCTATTCATACTTGGGCTCAATTAGAGAAACAATTTCATG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.10% | 0.40% | 18.07% | 15.45% | NA |
| All Indica | 2759 | 53.00% | 0.50% | 23.60% | 22.83% | NA |
| All Japonica | 1512 | 95.50% | 0.00% | 0.40% | 4.10% | NA |
| Aus | 269 | 21.90% | 0.70% | 68.40% | 8.92% | NA |
| Indica I | 595 | 31.30% | 0.50% | 14.79% | 53.45% | NA |
| Indica II | 465 | 73.30% | 1.10% | 16.13% | 9.46% | NA |
| Indica III | 913 | 53.90% | 0.30% | 34.17% | 11.61% | NA |
| Indica Intermediate | 786 | 56.50% | 0.50% | 22.39% | 20.61% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.26% | 0.39% | NA |
| Tropical Japonica | 504 | 88.90% | 0.00% | 0.79% | 10.32% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 6.25% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 0.00% | 7.78% | 15.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221679698 | G -> A | LOC_Os02g36060.1 | synonymous_variant ; p.Arg195Arg; LOW | synonymous_codon | Average:11.563; most accessible tissue: Minghui63 flag leaf, score: 18.084 | N | N | N | N |
| vg0221679698 | G -> DEL | LOC_Os02g36060.1 | N | frameshift_variant | Average:11.563; most accessible tissue: Minghui63 flag leaf, score: 18.084 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0221679698 | NA | 3.71E-06 | mr1544 | 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 |
| vg0221679698 | NA | 7.61E-06 | mr1904 | 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 |