| Variant ID: vg1207348516 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 7348516 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.31, others allele: 0.00, population size: 263. )
TCTTTGACATAATGGAACATCTTCCCTTGCACCTTGTGAGGCAAACAAAGTTCTGTGGTCCAGCATTCATGACGCAGATGTATTCTTGCGAAAGGTACCT[A/G,C]
GGGATCCTTAAGGGTTATGTACGGAACCGTTCACACCCCGAGGGGAGTATCATCGAGAGTTACACCACCGAAGAGGTCATCGATTTTTGTGTGGACTAGA
TCTAGTCCACACAAAAATCGATGACCTCTTCGGTGGTGTAACTCTCGATGATACTCCCCTCGGGGTGTGAACGGTTCCGTACATAACCCTTAAGGATCCC[T/C,G]
AGGTACCTTTCGCAAGAATACATCTGCGTCATGAATGCTGGACCACAGAACTTTGTTTGCCTCACAAGGTGCAAGGGAAGATGTTCCATTATGTCAAAGA
| 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 | 50.10% | 48.60% | 1.10% | 0.00% | C: 0.21% |
| All Indica | 2759 | 80.10% | 17.90% | 1.59% | 0.00% | C: 0.36% |
| All Japonica | 1512 | 4.90% | 95.00% | 0.13% | 0.00% | NA |
| Aus | 269 | 20.80% | 77.70% | 1.49% | 0.00% | NA |
| Indica I | 595 | 82.90% | 15.50% | 1.34% | 0.00% | C: 0.34% |
| Indica II | 465 | 84.90% | 14.40% | 0.65% | 0.00% | NA |
| Indica III | 913 | 82.40% | 15.00% | 2.41% | 0.00% | C: 0.22% |
| Indica Intermediate | 786 | 72.60% | 25.20% | 1.40% | 0.00% | C: 0.76% |
| Temperate Japonica | 767 | 4.70% | 95.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.90% | 97.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 22.20% | 75.60% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1207348516 | A -> C | LOC_Os12g13180.1 | synonymous_variant ; p.Leu632Leu; LOW | nonsynonymous_codon ; L632R | Average:34.41; most accessible tissue: Minghui63 young leaf, score: 51.901 | unknown | unknown | DELETERIOUS | 0.02 |
| vg1207348516 | A -> G | LOC_Os12g13180.1 | synonymous_variant ; p.Leu632Leu; LOW | nonsynonymous_codon ; L632R | Average:34.41; most accessible tissue: Minghui63 young leaf, score: 51.901 | unknown | unknown | DELETERIOUS | 0.02 |
| vg1207348516 | A -> G | LOC_Os12g13180.1 | synonymous_variant ; p.Leu632Leu; LOW | synonymous_codon | Average:34.41; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1207348516 | NA | 3.93E-06 | mr1261 | Ind_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 |
| vg1207348516 | 4.82E-06 | 4.82E-06 | mr1340 | 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 |
| vg1207348516 | 7.35E-06 | 7.35E-06 | mr1429 | Ind_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 |