| Variant ID: vg0322318094 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22318094 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GATTTGTTTTCTCTGAATTTTTCAGATTTGCTGCAGAGTCCAACAAAATTAAATAAAAGGTAAATCAAATTGCTTTACTTGTTTATATGAAATATATACT[G/A]
CTTCTAGGAGTTACATGTATGTTCAACTCTATTTGCAGTGTTAATTCTATGTTTTTTTTTAATTTTTGGACTGTAATTTGTTTTTATGTTGATTACTAGA
TCTAGTAATCAACATAAAAACAAATTACAGTCCAAAAATTAAAAAAAAACATAGAATTAACACTGCAAATAGAGTTGAACATACATGTAACTCCTAGAAG[C/T]
AGTATATATTTCATATAAACAAGTAAAGCAATTTGATTTACCTTTTATTTAATTTTGTTGGACTCTGCAGCAAATCTGAAAAATTCAGAGAAAACAAATC
| 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 | 93.80% | 2.40% | 3.34% | 0.44% | NA |
| All Indica | 2759 | 94.70% | 3.10% | 2.25% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 0.20% | 0.93% | 0.20% | NA |
| Aus | 269 | 63.20% | 8.20% | 28.25% | 0.37% | NA |
| Indica I | 595 | 98.70% | 0.30% | 1.01% | 0.00% | NA |
| Indica II | 465 | 98.50% | 0.40% | 1.08% | 0.00% | NA |
| Indica III | 913 | 91.00% | 5.70% | 3.29% | 0.00% | NA |
| Indica Intermediate | 786 | 93.60% | 3.70% | 2.67% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.40% | 0.60% | 2.58% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 77.10% | 3.10% | 3.12% | 16.67% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 3.33% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322318094 | G -> A | LOC_Os03g40160.1 | intron_variant ; MODIFIER | silent_mutation | Average:9.415; most accessible tissue: Zhenshan97 flower, score: 16.6 | N | N | N | N |
| vg0322318094 | G -> DEL | N | N | silent_mutation | Average:9.415; most accessible tissue: Zhenshan97 flower, score: 16.6 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0322318094 | NA | 1.41E-06 | mr1652 | 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 |
| vg0322318094 | 5.25E-06 | 3.64E-07 | mr1854 | 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 |