| Variant ID: vg0426938787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 26938787 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
GGTGTTAGTTGTTCAAACCTTATAGGTGCATGTTTTCTTTACAACCGACACCTATATATTGTTATATGTGCCGGTTATGTAACCGACACCGATGCCTTTA[G/T]
TCATCAGTGCCATCTGCTTGGATGCCGGTTGAGAAAACCAATACCTTTGTGTGGTTCCAACTAACACCTATTAATGTTTTTTTAGTAGTATTAATTTCAA
TTGAAATTAATACTACTAAAAAAACATTAATAGGTGTTAGTTGGAACCACACAAAGGTATTGGTTTTCTCAACCGGCATCCAAGCAGATGGCACTGATGA[C/A]
TAAAGGCATCGGTGTCGGTTACATAACCGGCACATATAACAATATATAGGTGTCGGTTGTAAAGAAAACATGCACCTATAAGGTTTGAACAACTAACACC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.20% | 3.20% | 0.55% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 88.90% | 9.90% | 1.19% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.20% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.00% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 94.80% | 3.70% | 1.56% | 0.00% | NA |
| Tropical Japonica | 504 | 91.50% | 8.30% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 64.70% | 33.20% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0426938787 | G -> T | LOC_Os04g45540.1 | upstream_gene_variant ; 1730.0bp to feature; MODIFIER | silent_mutation | Average:49.081; most accessible tissue: Callus, score: 76.052 | N | N | N | N |
| vg0426938787 | G -> T | LOC_Os04g45520-LOC_Os04g45540 | intergenic_region ; MODIFIER | silent_mutation | Average:49.081; most accessible tissue: Callus, score: 76.052 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0426938787 | NA | 3.03E-07 | mr1064 | 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 |
| vg0426938787 | NA | 3.16E-06 | mr1534 | 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 |
| vg0426938787 | 6.46E-06 | 9.36E-09 | mr1064_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 |