| Variant ID: vg1103943350 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 3943350 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAGTCTGCTGCGCCGAGAAATCCGCTCGGCTTCATTTTTGTCTTGAGGAAGTTCTTGTTTGCTCAAAAATTTTATGAACGGTTCTTTCCAGTCGGCTTCG[A/T]
TCATGCTCACGCCTTGAGTATCCATGGCTTCAATTGTCTCTTTTCTGGGCACGGTTGGTTCGTAAAGATGTTCAACGAACACATCTGATCTGAAGGAGCT
AGCTCCTTCAGATCAGATGTGTTCGTTGAACATCTTTACGAACCAACCGTGCCCAGAAAAGAGACAATTGAAGCCATGGATACTCAAGGCGTGAGCATGA[T/A]
CGAAGCCGACTGGAAAGAACCGTTCATAAAATTTTTGAGCAAACAAGAACTTCCTCAAGACAAAAATGAAGCCGAGCGGATTTCTCGGCGCAGCAGACTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.20% | 5.50% | 15.81% | 46.49% | NA |
| All Indica | 2759 | 6.40% | 5.90% | 19.28% | 68.39% | NA |
| All Japonica | 1512 | 86.60% | 0.90% | 4.43% | 8.07% | NA |
| Aus | 269 | 1.50% | 27.50% | 37.92% | 33.09% | NA |
| Indica I | 595 | 5.70% | 4.40% | 17.65% | 72.27% | NA |
| Indica II | 465 | 4.90% | 6.20% | 20.86% | 67.96% | NA |
| Indica III | 913 | 6.10% | 5.00% | 17.74% | 71.08% | NA |
| Indica Intermediate | 786 | 8.00% | 8.00% | 21.37% | 62.60% | NA |
| Temperate Japonica | 767 | 99.10% | 0.40% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 66.70% | 1.80% | 10.91% | 20.63% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.80% | 4.15% | 6.64% | NA |
| VI/Aromatic | 96 | 3.10% | 4.20% | 38.54% | 54.17% | NA |
| Intermediate | 90 | 32.20% | 5.60% | 10.00% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1103943350 | A -> T | LOC_Os11g07720.1 | downstream_gene_variant ; 4394.0bp to feature; MODIFIER | silent_mutation | Average:21.029; most accessible tissue: Callus, score: 29.032 | N | N | N | N |
| vg1103943350 | A -> T | LOC_Os11g07730.1 | intron_variant ; MODIFIER | silent_mutation | Average:21.029; most accessible tissue: Callus, score: 29.032 | N | N | N | N |
| vg1103943350 | A -> DEL | N | N | silent_mutation | Average:21.029; most accessible tissue: Callus, score: 29.032 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1103943350 | 1.33E-06 | NA | mr1298 | 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 |
| vg1103943350 | NA | 5.39E-07 | mr1532 | 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 |
| vg1103943350 | NA | 8.17E-08 | mr1659 | 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 |
| vg1103943350 | 9.42E-06 | NA | mr1731 | 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 |