| Variant ID: vg1116397469 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16397469 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 51. )
TTAGGTTCACTAAAGAACGGATCATAGCCATATACTACTAGGCAAAATTTGTTGCAGGACATCTAAACAACGTGCAAGAACACGTTTATGCTATAGGGCA[C/T]
TATAAAAAAGTGGTAATTAGTTGCTCGATACACACAACATTATTTTATTATATCCGGAGGAATTGGAAAGTGAAACCGCTGCGAAAGTATGTTTTTACCC
GGGTAAAAACATACTTTCGCAGCGGTTTCACTTTCCAATTCCTCCGGATATAATAAAATAATGTTGTGTGTATCGAGCAACTAATTACCACTTTTTTATA[G/A]
TGCCCTATAGCATAAACGTGTTCTTGCACGTTGTTTAGATGTCCTGCAACAAATTTTGCCTAGTAGTATATGGCTATGATCCGTTCTTTAGTGAACCTAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.00% | 20.00% | 0.42% | 14.64% | NA |
| All Indica | 2759 | 78.10% | 5.90% | 0.62% | 15.37% | NA |
| All Japonica | 1512 | 43.60% | 47.00% | 0.13% | 9.26% | NA |
| Aus | 269 | 68.80% | 2.60% | 0.00% | 28.62% | NA |
| Indica I | 595 | 75.80% | 7.90% | 0.50% | 15.80% | NA |
| Indica II | 465 | 91.80% | 3.40% | 0.00% | 4.73% | NA |
| Indica III | 913 | 72.40% | 5.90% | 0.33% | 21.36% | NA |
| Indica Intermediate | 786 | 78.50% | 5.70% | 1.40% | 14.38% | NA |
| Temperate Japonica | 767 | 15.10% | 68.20% | 0.13% | 16.56% | NA |
| Tropical Japonica | 504 | 72.20% | 26.40% | 0.20% | 1.19% | NA |
| Japonica Intermediate | 241 | 74.30% | 22.80% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 11.50% | 50.00% | 1.04% | 37.50% | NA |
| Intermediate | 90 | 66.70% | 16.70% | 0.00% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116397469 | C -> T | LOC_Os11g28480.1 | upstream_gene_variant ; 2274.0bp to feature; MODIFIER | silent_mutation | Average:45.246; most accessible tissue: Callus, score: 87.071 | N | N | N | N |
| vg1116397469 | C -> T | LOC_Os11g28480-LOC_Os11g28490 | intergenic_region ; MODIFIER | silent_mutation | Average:45.246; most accessible tissue: Callus, score: 87.071 | N | N | N | N |
| vg1116397469 | C -> DEL | N | N | silent_mutation | Average:45.246; most accessible tissue: Callus, score: 87.071 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116397469 | NA | 8.92E-08 | mr1229 | Jap_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 |
| vg1116397469 | 1.27E-06 | 7.30E-07 | mr1530 | 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 |
| vg1116397469 | NA | 1.46E-08 | mr1530 | Jap_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 |
| vg1116397469 | NA | 9.36E-09 | mr1629 | Jap_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 |
| vg1116397469 | NA | 1.50E-06 | mr1982 | Jap_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 |