| Variant ID: vg1119522374 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 19522374 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 93. )
ATGGATTTCAGGAGATCGGCACAGCCATCGTCTGGGATCCCGATTGTTCGATCGGAGCAAGTGCAAGCACACCATATTGCGGACTCTAGCGACGACTAGC[G/A]
TCACTAGCCTCTCCGAGGTGTGCATATGCACCATACGACTGCCTGGGCAAAGAAGATAAGATTGATATGATATACACGACATAAGAAATAATTAAGTAGT
ACTACTTAATTATTTCTTATGTCGTGTATATCATATCAATCTTATCTTCTTTGCCCAGGCAGTCGTATGGTGCATATGCACACCTCGGAGAGGCTAGTGA[C/T]
GCTAGTCGTCGCTAGAGTCCGCAATATGGTGTGCTTGCACTTGCTCCGATCGAACAATCGGGATCCCAGACGATGGCTGTGCCGATCTCCTGAAATCCAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.50% | 39.90% | 1.93% | 6.62% | NA |
| All Indica | 2759 | 77.90% | 10.80% | 2.39% | 8.92% | NA |
| All Japonica | 1512 | 1.30% | 96.60% | 0.20% | 1.92% | NA |
| Aus | 269 | 84.00% | 5.60% | 5.20% | 5.20% | NA |
| Indica I | 595 | 84.70% | 8.90% | 3.19% | 3.19% | NA |
| Indica II | 465 | 71.00% | 24.90% | 3.01% | 1.08% | NA |
| Indica III | 913 | 76.60% | 3.20% | 1.42% | 18.84% | NA |
| Indica Intermediate | 786 | 78.20% | 12.80% | 2.54% | 6.36% | NA |
| Temperate Japonica | 767 | 1.30% | 96.20% | 0.13% | 2.35% | NA |
| Tropical Japonica | 504 | 1.20% | 96.80% | 0.40% | 1.59% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.10% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 6.20% | 72.90% | 1.04% | 19.79% | NA |
| Intermediate | 90 | 38.90% | 47.80% | 7.78% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1119522374 | G -> A | LOC_Os11g33030.1 | upstream_gene_variant ; 1408.0bp to feature; MODIFIER | silent_mutation | Average:33.194; most accessible tissue: Callus, score: 84.946 | N | N | N | N |
| vg1119522374 | G -> A | LOC_Os11g33020.1 | downstream_gene_variant ; 1342.0bp to feature; MODIFIER | silent_mutation | Average:33.194; most accessible tissue: Callus, score: 84.946 | N | N | N | N |
| vg1119522374 | G -> A | LOC_Os11g33020-LOC_Os11g33030 | intergenic_region ; MODIFIER | silent_mutation | Average:33.194; most accessible tissue: Callus, score: 84.946 | N | N | N | N |
| vg1119522374 | G -> DEL | N | N | silent_mutation | Average:33.194; most accessible tissue: Callus, score: 84.946 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1119522374 | NA | 1.01E-06 | mr1044 | 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 |
| vg1119522374 | NA | 1.64E-06 | mr1077 | 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 |
| vg1119522374 | NA | 3.82E-06 | mr1149 | 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 |
| vg1119522374 | 1.09E-06 | 3.54E-08 | mr1648 | 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 |