| Variant ID: vg0401798478 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1798478 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGCGAAGAAGAAGTGCCCACGACCAAGGTCTCGAAGAGCGGAGAAAGCGAAGCTAAGACCAAAAAGATTTCCCTAGATCCTTCTGATCCCACTAAAACTG[C/T]
TGTAATAGGCTCCGAGTTAGACTGTAAATAGGAAAGCGCGCTCATCACCTTTCTTCAAAATAATAAAGATATCTTTGCGTGGAAACCATCTGATATGCCT
AGGCATATCAGATGGTTTCCACGCAAAGATATCTTTATTATTTTGAAGAAAGGTGATGAGCGCGCTTTCCTATTTACAGTCTAACTCGGAGCCTATTACA[G/A]
CAGTTTTAGTGGGATCAGAAGGATCTAGGGAAATCTTTTTGGTCTTAGCTTCGCTTTCTCCGCTCTTCGAGACCTTGGTCGTGGGCACTTCTTCTTCGCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.00% | 0.30% | 6.92% | 67.80% | NA |
| All Indica | 2759 | 15.90% | 0.40% | 7.87% | 75.79% | NA |
| All Japonica | 1512 | 45.90% | 0.10% | 2.25% | 51.79% | NA |
| Aus | 269 | 9.30% | 0.00% | 18.22% | 72.49% | NA |
| Indica I | 595 | 4.50% | 0.20% | 5.04% | 90.25% | NA |
| Indica II | 465 | 31.00% | 0.40% | 12.47% | 56.13% | NA |
| Indica III | 913 | 16.50% | 0.40% | 7.45% | 75.58% | NA |
| Indica Intermediate | 786 | 14.90% | 0.60% | 7.76% | 76.72% | NA |
| Temperate Japonica | 767 | 75.70% | 0.00% | 0.65% | 23.60% | NA |
| Tropical Japonica | 504 | 7.70% | 0.20% | 3.97% | 88.10% | NA |
| Japonica Intermediate | 241 | 30.70% | 0.00% | 3.73% | 65.56% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 19.79% | 77.08% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 8.89% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401798478 | C -> DEL | N | N | silent_mutation | Average:15.082; most accessible tissue: Callus, score: 30.303 | N | N | N | N |
| vg0401798478 | C -> T | LOC_Os04g03930.1 | upstream_gene_variant ; 3495.0bp to feature; MODIFIER | silent_mutation | Average:15.082; most accessible tissue: Callus, score: 30.303 | N | N | N | N |
| vg0401798478 | C -> T | LOC_Os04g03950.1 | downstream_gene_variant ; 3517.0bp to feature; MODIFIER | silent_mutation | Average:15.082; most accessible tissue: Callus, score: 30.303 | N | N | N | N |
| vg0401798478 | C -> T | LOC_Os04g03940.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.082; most accessible tissue: Callus, score: 30.303 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401798478 | 2.15E-06 | 2.07E-06 | mr1666_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 |