| Variant ID: vg0823030389 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23030389 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGAGAAAAGACTGAGAGGAGAGGATAAGATTGGGTTAGGTGTGAAATTTTTTGAACTGCGGAAGAGGGACCATTTTTACATGCGGGCTACGGAAGAGGGA[G/A]
GGAAGTTACATAACTTTGTTATTAATGACTTTTTCAGATGAAATCATTTACTGCTTCAAAATATTATTTGAAGTTTTGAAATTCAAATTTTTATTTGATA
TATCAAATAAAAATTTGAATTTCAAAACTTCAAATAATATTTTGAAGCAGTAAATGATTTCATCTGAAAAAGTCATTAATAACAAAGTTATGTAACTTCC[C/T]
TCCCTCTTCCGTAGCCCGCATGTAAAAATGGTCCCTCTTCCGCAGTTCAAAAAATTTCACACCTAACCCAATCTTATCCTCTCCTCTCAGTCTTTTCTCT
| 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 | 73.20% | 21.80% | 4.27% | 0.74% | NA |
| All Indica | 2759 | 95.50% | 0.50% | 2.72% | 1.27% | NA |
| All Japonica | 1512 | 26.70% | 65.70% | 7.54% | 0.00% | NA |
| Aus | 269 | 97.40% | 1.10% | 1.49% | 0.00% | NA |
| Indica I | 595 | 94.30% | 0.20% | 4.37% | 1.18% | NA |
| Indica II | 465 | 92.30% | 0.90% | 4.30% | 2.58% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.11% | 0.22% | NA |
| Indica Intermediate | 786 | 93.40% | 1.30% | 3.56% | 1.78% | NA |
| Temperate Japonica | 767 | 5.30% | 92.70% | 1.96% | 0.00% | NA |
| Tropical Japonica | 504 | 62.90% | 19.00% | 18.06% | 0.00% | NA |
| Japonica Intermediate | 241 | 19.10% | 77.60% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 15.60% | 8.89% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823030389 | G -> A | LOC_Os08g36480.1 | upstream_gene_variant ; 2841.0bp to feature; MODIFIER | silent_mutation | Average:45.277; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0823030389 | G -> A | LOC_Os08g36470-LOC_Os08g36480 | intergenic_region ; MODIFIER | silent_mutation | Average:45.277; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0823030389 | G -> DEL | N | N | silent_mutation | Average:45.277; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0823030389 | NA | 5.06E-08 | mr1514 | 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 |
| vg0823030389 | NA | 3.77E-08 | mr1806 | 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 |
| vg0823030389 | NA | 1.60E-21 | mr1276_2 | 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 |
| vg0823030389 | NA | 2.66E-21 | mr1682_2 | 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 |
| vg0823030389 | NA | 4.06E-06 | mr1780_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 |