| Variant ID: vg1103943395 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 3943395 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 63. )
AGGAAGTTCTTGTTTGCTCAAAAATTTTATGAACGGTTCTTTCCAGTCGGCTTCGATCATGCTCACGCCTTGAGTATCCATGGCTTCAATTGTCTCTTTT[C/T]
TGGGCACGGTTGGTTCGTAAAGATGTTCAACGAACACATCTGATCTGAAGGAGCTGCTTCCCGTTTTGAACCAAAATTGGCCAGCCTGTCGGCTGCCTCA
TGAGGCAGCCGACAGGCTGGCCAATTTTGGTTCAAAACGGGAAGCAGCTCCTTCAGATCAGATGTGTTCGTTGAACATCTTTACGAACCAACCGTGCCCA[G/A]
AAAAGAGACAATTGAAGCCATGGATACTCAAGGCGTGAGCATGATCGAAGCCGACTGGAAAGAACCGTTCATAAAATTTTTGAGCAAACAAGAACTTCCT
| 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 | 32.30% | 13.50% | 16.31% | 37.88% | NA |
| All Indica | 2759 | 6.50% | 15.50% | 22.11% | 55.85% | NA |
| All Japonica | 1512 | 86.50% | 3.20% | 3.04% | 7.21% | NA |
| Aus | 269 | 2.20% | 50.20% | 23.79% | 23.79% | NA |
| Indica I | 595 | 5.70% | 11.30% | 28.74% | 54.29% | NA |
| Indica II | 465 | 5.40% | 11.00% | 22.80% | 60.86% | NA |
| Indica III | 913 | 5.90% | 18.80% | 16.76% | 58.49% | NA |
| Indica Intermediate | 786 | 8.50% | 17.60% | 22.90% | 51.02% | NA |
| Temperate Japonica | 767 | 99.10% | 0.30% | 0.39% | 0.26% | NA |
| Tropical Japonica | 504 | 66.50% | 7.50% | 7.34% | 18.65% | NA |
| Japonica Intermediate | 241 | 88.40% | 3.70% | 2.49% | 5.39% | NA |
| VI/Aromatic | 96 | 3.10% | 18.80% | 37.50% | 40.62% | NA |
| Intermediate | 90 | 33.30% | 8.90% | 16.67% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1103943395 | C -> T | LOC_Os11g07730.1 | missense_variant ; p.Glu1238Lys; MODERATE | nonsynonymous_codon ; E1238K | Average:28.23; most accessible tissue: Minghui63 flag leaf, score: 36.591 | unknown | unknown | DELETERIOUS | 0.01 |
| vg1103943395 | C -> DEL | LOC_Os11g07730.1 | N | frameshift_variant | Average:28.23; most accessible tissue: Minghui63 flag leaf, score: 36.591 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1103943395 | NA | 9.49E-06 | 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 |
| vg1103943395 | NA | 3.64E-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 |
| vg1103943395 | 2.63E-06 | 9.54E-09 | mr1806 | 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 |