| Variant ID: vg0412754396 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 12754396 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGCTAAGGTTTCGGCTAGCACTCAGCAAACAAGAAAGGGGATAAACTAGATTGAAATTCCCCATTATCAAGCAAAAGGGAATAAACAAGATTGAAATTT[C/G]
CCGAAATCCCCAATAAGCCGGATCCAATTGGCCTAAAATCCCCAAATGAGGAAGCCTAATTTTTGGGGGAAGAACCCTAAGTCACAAATATCCGAATTAA
TTAATTCGGATATTTGTGACTTAGGGTTCTTCCCCCAAAAATTAGGCTTCCTCATTTGGGGATTTTAGGCCAATTGGATCCGGCTTATTGGGGATTTCGG[G/C]
AAATTTCAATCTTGTTTATTCCCTTTTGCTTGATAATGGGGAATTTCAATCTAGTTTATCCCCTTTCTTGTTTGCTGAGTGCTAGCCGAAACCTTAGCAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.10% | 1.60% | 3.11% | 60.20% | NA |
| All Indica | 2759 | 5.50% | 0.00% | 3.19% | 91.34% | NA |
| All Japonica | 1512 | 90.30% | 4.80% | 3.11% | 1.72% | NA |
| Aus | 269 | 3.00% | 0.00% | 1.49% | 95.54% | NA |
| Indica I | 595 | 5.20% | 0.00% | 2.52% | 92.27% | NA |
| Indica II | 465 | 9.20% | 0.00% | 1.29% | 89.46% | NA |
| Indica III | 913 | 3.00% | 0.00% | 5.70% | 91.35% | NA |
| Indica Intermediate | 786 | 6.40% | 0.00% | 1.91% | 91.73% | NA |
| Temperate Japonica | 767 | 84.00% | 8.90% | 5.61% | 1.56% | NA |
| Tropical Japonica | 504 | 98.60% | 0.20% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 93.40% | 1.70% | 1.66% | 3.32% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 0.00% | 9.38% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 8.89% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0412754396 | C -> DEL | N | N | silent_mutation | Average:9.4; most accessible tissue: Callus, score: 23.619 | N | N | N | N |
| vg0412754396 | C -> G | LOC_Os04g22510.1 | upstream_gene_variant ; 3730.0bp to feature; MODIFIER | silent_mutation | Average:9.4; most accessible tissue: Callus, score: 23.619 | N | N | N | N |
| vg0412754396 | C -> G | LOC_Os04g22510-LOC_Os04g22520 | intergenic_region ; MODIFIER | silent_mutation | Average:9.4; most accessible tissue: Callus, score: 23.619 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0412754396 | 8.77E-07 | 1.13E-08 | mr1062_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 |