| Variant ID: vg1118218762 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 18218762 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 70. )
CCTTGGCAAAGGATACTTGTTCTTGATGGTGACCTCATTGAGTGCGCGGTAGTCAACGCACATCCTCTTGGTTTTGTCTTTCTTCTCCACAAAGATAACC[A/G]
GAGCACCCCAAGGTGACGTGCTCGGGCGGATGTATCCCAAGGTAACTGTTCATCGACTTGTTTCTTGACTTCCGCCAACTCGTTGGCTCCCATTCTGTAA
TTACAGAATGGGAGCCAACGAGTTGGCGGAAGTCAAGAAACAAGTCGATGAACAGTTACCTTGGGATACATCCGCCCGAGCACGTCACCTTGGGGTGCTC[T/C]
GGTTATCTTTGTGGAGAAGAAAGACAAAACCAAGAGGATGTGCGTTGACTACCGCGCACTCAATGAGGTCACCATCAAGAACAAGTATCCTTTGCCAAGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.50% | 4.20% | 16.46% | 62.89% | NA |
| All Indica | 2759 | 5.40% | 5.00% | 17.25% | 72.38% | NA |
| All Japonica | 1512 | 38.30% | 3.30% | 12.43% | 45.97% | NA |
| Aus | 269 | 4.50% | 1.50% | 18.22% | 75.84% | NA |
| Indica I | 595 | 2.20% | 17.00% | 14.45% | 66.39% | NA |
| Indica II | 465 | 10.30% | 0.90% | 10.75% | 78.06% | NA |
| Indica III | 913 | 3.00% | 0.30% | 21.36% | 75.36% | NA |
| Indica Intermediate | 786 | 7.60% | 3.80% | 18.45% | 70.10% | NA |
| Temperate Japonica | 767 | 61.10% | 5.50% | 5.48% | 27.90% | NA |
| Tropical Japonica | 504 | 3.00% | 1.20% | 22.02% | 73.81% | NA |
| Japonica Intermediate | 241 | 39.40% | 0.80% | 14.52% | 45.23% | NA |
| VI/Aromatic | 96 | 29.20% | 3.10% | 46.88% | 20.83% | NA |
| Intermediate | 90 | 13.30% | 2.20% | 22.22% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1118218762 | A -> DEL | N | N | silent_mutation | Average:18.825; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| vg1118218762 | A -> G | LOC_Os11g31240.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:18.825; most accessible tissue: Minghui63 young leaf, score: 43.347 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1118218762 | NA | 4.93E-06 | mr1961_2 | Ind_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 |